{
  "twilight": {
    "Depends": [
      "R (>= 2.1.0)",
      "splines (>= 2.2.0)",
      "stats (>= 2.2.0)",
      "Biobase(>= 1.12.0)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/twilight_1.26.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/twilight_1.26.0.tgz",
    "Version": "1.26.0",
    "dependsOnMe": [
      "OrderedList"
    ],
    "URL": "http://compdiag.molgen.mpg.de/software/twilight.shtml",
    "Maintainer": "Stefanie Scheid <stefanie.scheid@gmx.de>",
    "Author": "Stefanie Scheid <stefanie.scheid@gmx.de>",
    "Title": "Estimation of local false discovery rate",
    "source.ver": "src/contrib/twilight_1.26.0.tar.gz",
    "Imports": [
      "Biobase",
      "graphics",
      "grDevices",
      "stats"
    ],
    "Suggests": [
      "golubEsets (>= 1.4.2)",
      "vsn (>= 1.7.2)"
    ],
    "Package": "twilight",
    "vignettes": [
      "vignettes/twilight/inst/doc/bcb_logo.pdf",
      "vignettes/twilight/inst/doc/Rplots.pdf",
      "vignettes/twilight/inst/doc/tr_2004_01.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL (>= 2)",
    "biocViews": [
      "Bioinformatics",
      "DifferentialExpression",
      "Microarray",
      "MultipleComparisons",
      "Software"
    ],
    "Description": "In a typical microarray setting with gene expression data observed under two conditions, the local false discovery rate describes the probability that a gene is not differentially expressed between the two conditions given its corrresponding observed score or p-value level. The resulting curve of p-values versus local false discovery rate offers an insight into the twilight zone between clear differential and clear non-differential gene expression. Package 'twilight' contains two main functions: Function twilight.pval performs a two-condition test on differences in means for a given input matrix or expression set and computes permutation based p-values. Function twilight performs a stochastic downhill search to estimate local false discovery rates and effect size distributions. The package further provides means to filter for permutations that describe the null distribution correctly. Using filtered permutations, the influence of hidden confounders could be diminished.",
    "importsMe": [
      "OrderedList"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/twilight_1.26.0.zip"
  },
  "OutlierD": {
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      "R (>= 2.3.0)",
      "Biobase",
      "quantreg"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/OutlierD_1.14.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/OutlierD_1.14.0.tgz",
    "Version": "1.14.0",
    "URL": "http://www.korea.ac.kr/~stat2242/",
    "Maintainer": "Sukwoo Kim <s4kim@korea.ac.kr>",
    "Author": "HyungJun Cho <hj4cho@korea.ac.kr>",
    "Title": "Outlier detection using quantile regression on the M-A scatterplots of high-throughput data",
    "source.ver": "src/contrib/OutlierD_1.14.0.tar.gz",
    "Package": "OutlierD",
    "vignettes": [
      "vignettes/OutlierD/inst/doc/OutlierD.pdf"
    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "Bioinformatics",
      "Microarray",
      "Software"
    ],
    "Description": "This package detects outliers using quantile regression on the M-A scatterplots of high-throughput data.",
    "win.binary.ver": "bin/windows/contrib/2.12/OutlierD_1.14.0.zip"
  },
  "codelink": {
    "Depends": [
      "methods",
      "Biobase (>= 2.5.5)",
      "limma"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/codelink_1.18.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/codelink_1.18.0.tgz",
    "Version": "1.18.0",
    "URL": "http://www.kuicr.kyoto-u.ac.jp/~diez",
    "Maintainer": "Diego Diez <diez@kuicr.kyoto-u.ac.jp>",
    "Author": "Diego Diez <diez@kuicr.kyoto-u.ac.jp>",
    "Title": "Manipulation of Codelink Bioarrays data.",
    "suggestsMe": [
      "AgiMicroRna",
      "MAQCsubset"
    ],
    "source.ver": "src/contrib/codelink_1.18.0.tar.gz",
    "Imports": [
      "annotate"
    ],
    "Suggests": [
      "genefilter"
    ],
    "Package": "codelink",
    "vignettes": [
      "vignettes/codelink/inst/doc/codelink.pdf",
      "vignettes/codelink/inst/doc/CodelinkSet.pdf"
    ],
    "License": "GPL",
    "biocViews": [
      "DataImport",
      "Microarray",
      "OneChannel",
      "Preprocessing",
      "Software"
    ],
    "Description": "This packages allow reading into R of Codelink bioarray data exported as text from the Codelink software. Also includes some functions to ease the manipulation and pre-processing of data, such in background correction and normalization.",
    "Enhances": [
      "multicore"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/codelink_1.18.0.zip"
  },
  "Genominator": {
    "Depends": [
      "methods",
      "RSQLite",
      "DBI (>= 0.2-5)",
      "IRanges",
      "GenomeGraphs"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/Genominator_1.4.2.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/Genominator_1.4.2.tgz",
    "Version": "1.4.2",
    "Maintainer": "James Bullard <bullard@stat.berkeley.edu>",
    "Author": "James Bullard, Kasper Daniel Hansen",
    "Title": "Analyze, manage and store genomic data",
    "suggestsMe": [
      "oneChannelGUI"
    ],
    "source.ver": "src/contrib/Genominator_1.4.2.tar.gz",
    "Imports": [
      "graphics",
      "stats",
      "utils"
    ],
    "Suggests": [
      "biomaRt",
      "ShortRead",
      "yeastRNASeq"
    ],
    "Package": "Genominator",
    "vignettes": [
      "vignettes/Genominator/inst/doc/Genominator.pdf",
      "vignettes/Genominator/inst/doc/plotting.pdf",
      "vignettes/Genominator/inst/doc/withShortRead.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "Software",
      "Visualization"
    ],
    "Description": "Tools for storing, accessing, analyzing and visualizing genomic data.",
    "win.binary.ver": "bin/windows/contrib/2.12/Genominator_1.4.2.zip"
  },
  "diffGeneAnalysis": {
    "win64.binary.ver": "bin/windows64/contrib/2.12/diffGeneAnalysis_1.32.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/diffGeneAnalysis_1.32.0.tgz",
    "Version": "1.32.0",
    "Maintainer": "Choudary Jagarlamudi <choudary.jagar@swosu.edu>",
    "Author": "Choudary Jagarlamudi",
    "Title": "Performs differential gene expression Analysis",
    "source.ver": "src/contrib/diffGeneAnalysis_1.32.0.tar.gz",
    "Imports": [
      "graphics",
      "grDevices",
      "minpack.lm (>= 1.0-4)",
      "stats",
      "utils"
    ],
    "Package": "diffGeneAnalysis",
    "vignettes": [
      "vignettes/diffGeneAnalysis/inst/doc/diffGeneAnalysis.pdf"
    ],
    "License": "GPL",
    "biocViews": [
      "Bioinformatics",
      "DifferentialExpression",
      "Microarray",
      "Software"
    ],
    "Description": "Analyze microarray data",
    "win.binary.ver": "bin/windows/contrib/2.12/diffGeneAnalysis_1.32.0.zip"
  },
  "apComplex": {
    "Depends": [
      "graph",
      "RBGL"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/apComplex_2.16.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/apComplex_2.16.0.tgz",
    "Version": "2.16.0",
    "dependsOnMe": [
      "ScISI",
      "simulatorAPMS"
    ],
    "Maintainer": "Denise Scholtens <dscholtens@northwestern.edu>",
    "Author": "Denise Scholtens <dscholtens@northwestern.edu>",
    "Title": "Estimate protein complex membership using AP-MS protein data",
    "suggestsMe": [
      "BiocCaseStudies"
    ],
    "source.ver": "src/contrib/apComplex_2.16.0.tar.gz",
    "Imports": [
      "Rgraphviz",
      "stats",
      "org.Sc.sgd.db"
    ],
    "Package": "apComplex",
    "vignettes": [
      "vignettes/apComplex/inst/doc/apComplex.pdf"
    ],
    "License": "LGPL",
    "biocViews": [
      "GraphsAndNetworks",
      "MassSpectrometry",
      "Software",
      "Visualization"
    ],
    "Description": "Functions to estimate a bipartite graph of protein complex membership using AP-MS data.",
    "win.binary.ver": "bin/windows/contrib/2.12/apComplex_2.16.0.zip"
  },
  "oneChannelGUI": {
    "Depends": [
      "Biobase",
      "limma",
      "affylmGUI",
      "tkWidgets",
      "GOstats",
      "AnnotationDbi",
      "preprocessCore",
      "IRanges",
      "edgeR",
      "baySeq",
      "girafe"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/oneChannelGUI_1.16.5.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/oneChannelGUI_1.16.5.tgz",
    "Version": "1.16.5",
    "URL": "http://www.bioinformatica.unito.it/oneChannelGUI/",
    "Maintainer": "Raffaele A Calogero <raffaele.calogero@unito.it>",
    "Author": "Raffale A Calogero, Bioinformatics and Genomics Unit, Dept. of Clinical and Biological Sciences Torino (Italy)",
    "Title": "This package extends the capabilities of affylmGUI graphical interface. Affymetrix 3' IVT, gene an exon arrays are actually implemented togheter with Illumina, GEO matrix series files and tab delimited files. Next Generation Sequencing secondary analysis for ncRNA quantification is also available.",
    "source.ver": "src/contrib/oneChannelGUI_1.16.5.tar.gz",
    "Suggests": [
      "annotate",
      "genefilter",
      "maSigPro",
      "pamr",
      "pdmclass",
      "ChIPpeakAnno",
      "chipseq",
      "BSgenome",
      "Rgraphviz",
      "affy",
      "annaffy",
      "affyPLM",
      "multtest",
      "ssize",
      "sizepower",
      "siggenes",
      "RankProd",
      "org.Hs.eg.db",
      "org.Mm.eg.db",
      "org.Rn.eg.db",
      "metaArray",
      "MergeMaid",
      "biomaRt",
      "GenomeGraphs",
      "AffyCompatible",
      "Biostrings",
      "IRanges",
      "rtracklayer",
      "Genominator",
      "hugene10sttranscriptcluster.db",
      "mogene10sttranscriptcluster.db",
      "ragene10sttranscriptcluster.db",
      "HuExExonProbesetLocationHg19",
      "MoExExonProbesetLocation",
      "RaExExonProbesetLocation",
      "snow",
      "RmiR",
      "RmiR.Hs.miRNA"
    ],
    "Package": "oneChannelGUI",
    "vignettes": [
      "vignettes/oneChannelGUI/inst/doc/fignew42.pdf",
      "vignettes/oneChannelGUI/inst/doc/install.pdf",
      "vignettes/oneChannelGUI/inst/doc/NGS.pdf",
      "vignettes/oneChannelGUI/inst/doc/oneChannelGUI.pdf",
      "vignettes/oneChannelGUI/inst/doc/standAloneFunctions.pdf",
      "vignettes/oneChannelGUI/inst/doc/whatIsNew.pdf"
    ],
    "License": "The Artistic License, Version 2.0",
    "biocViews": [
      "DataImport",
      "DifferentialExpression",
      "HighThroughputSequencing",
      "Microarray",
      "MultipleComparisons",
      "OneChannel",
      "Preprocessing",
      "QualityControl",
      "RNAseq",
      "Software",
      "Statistics"
    ],
    "Description": "This package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code. This library provides a graphical interface for microarray gene and exon level analysis as well as basic secondary analysis of NGS data for ncRNA quantification.",
    "win.binary.ver": "bin/windows/contrib/2.12/oneChannelGUI_1.16.5.zip"
  },
  "GraphAT": {
    "Depends": [
      "graph",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/GraphAT_1.22.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/GraphAT_1.22.0.tgz",
    "Version": "1.22.0",
    "Maintainer": "Thomas LaFramboise <tlaframb@hsph.harvard.edu>",
    "Author": "R. Balasubramanian, T. LaFramboise, D. Scholtens",
    "Title": "Graph Theoretic Association Tests",
    "source.ver": "src/contrib/GraphAT_1.22.0.tar.gz",
    "Imports": [
      "graph",
      "MCMCpack",
      "methods",
      "stats"
    ],
    "Package": "GraphAT",
    "License": "LGPL",
    "biocViews": [
      "Bioinformatics",
      "GraphsAndNetworks",
      "Software"
    ],
    "Description": "Functions and data used in Balasubramanian, et al. (2004)",
    "win.binary.ver": "bin/windows/contrib/2.12/GraphAT_1.22.0.zip"
  },
  "BHC": {
    "win64.binary.ver": "bin/windows64/contrib/2.12/BHC_1.2.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/BHC_1.2.0.tgz",
    "Version": "1.2.0",
    "Maintainer": "Rich Savage <r.s.savage@warwick.ac.uk>",
    "Author": "Rich Savage (C++ code originally written by Yang Xu)",
    "Title": "Bayesian Hierarchical Clustering",
    "source.ver": "src/contrib/BHC_1.2.0.tar.gz",
    "Imports": [
      "stats",
      "utils"
    ],
    "Suggests": [
      "affydata",
      "gcrma",
      "graphics"
    ],
    "Package": "BHC",
    "vignettes": [
      "vignettes/BHC/inst/doc/bhc.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL-3",
    "biocViews": [
      "Clustering",
      "Microarray",
      "Software"
    ],
    "Description": "The method performs bottom-up hierarchical clustering, using a Dirichlet Process (infinite mixture) to model uncertainty in the data and Bayesian model selection to decide at each step which clusters to merge.  This avoids several limitations of traditional methods, for example how many clusters there should be and how to choose a principled distance metric.  This implementation accepts multinomial (i.e. discrete, with 2+ categories) data.",
    "win.binary.ver": "bin/windows/contrib/2.12/BHC_1.2.0.zip"
  },
  "EBarrays": {
    "Depends": [
      "R (>= 1.8.0)",
      "Biobase",
      "lattice",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/EBarrays_2.14.1.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/EBarrays_2.14.1.tgz",
    "Version": "2.14.1",
    "Maintainer": "Ming Yuan <myuan@isye.gatech.edu>",
    "Author": "Ming Yuan, Christina Kendziorski, Michael Newton and Deepayan Sarkar",
    "Title": "Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification",
    "suggestsMe": [
      "Category"
    ],
    "source.ver": "src/contrib/EBarrays_2.14.1.tar.gz",
    "Imports": [
      "Biobase",
      "cluster",
      "graphics",
      "grDevices",
      "lattice",
      "methods",
      "stats"
    ],
    "Package": "EBarrays",
    "vignettes": [
      "vignettes/EBarrays/inst/doc/vignette.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL (>= 2)",
    "biocViews": [
      "Clustering",
      "DifferentialExpression",
      "Software"
    ],
    "Description": "EBarrays provides tools for the analysis of replicated/unreplicated microarray data.",
    "win.binary.ver": "bin/windows/contrib/2.12/EBarrays_2.14.1.zip"
  },
  "affylmGUI": {
    "Depends": [
      "limma",
      "tcltk",
      "affy",
      "Biobase",
      "affyio"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/affylmGUI_1.24.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/affylmGUI_1.24.0.tgz",
    "Version": "1.24.0",
    "dependsOnMe": [
      "oneChannelGUI"
    ],
    "URL": "http://bioinf.wehi.edu.au/affylmGUI/",
    "Maintainer": "Keith Satterley <keith@wehi.edu.au>",
    "Author": "James Wettenhall and Ken Simpson Division of Genetics and Bioinformatics, WEHI.",
    "Title": "GUI for affy analysis using limma package",
    "source.ver": "src/contrib/affylmGUI_1.24.0.tar.gz",
    "Suggests": [
      "tkrplot",
      "affyPLM",
      "R2HTML",
      "xtable"
    ],
    "Package": "affylmGUI",
    "vignettes": [
      "vignettes/affylmGUI/inst/doc/affylmGUI.pdf",
      "vignettes/affylmGUI/inst/doc/extract.pdf"
    ],
    "License": "LGPL",
    "biocViews": [
      "Bioinformatics",
      "DataImport",
      "DifferentialExpression",
      "GUI",
      "Microarray",
      "MultipleComparisons",
      "OneChannel",
      "Preprocessing",
      "QualityControl",
      "Software"
    ],
    "Description": "A Graphical User Interface for affy analysis using the limma Microarray package",
    "win.binary.ver": "bin/windows/contrib/2.12/affylmGUI_1.24.0.zip"
  },
  "BioNet": {
    "Depends": [
      "R (>= 2.11.0)",
      "Biobase",
      "graph",
      "RBGL"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/BioNet_1.8.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/BioNet_1.8.0.tgz",
    "Version": "1.8.0",
    "dependsOnMe": [
      "HTSanalyzeR"
    ],
    "URL": "http://bionet.bioapps.biozentrum.uni-wuerzburg.de/",
    "Maintainer": "Marcus Dittrich <marcus.dittrich@biozentrum.uni-wuerzburg.de>",
    "Author": "Marcus Dittrich and Daniela Beisser",
    "Title": "Routines for the functional analysis of biological networks",
    "source.ver": "src/contrib/BioNet_1.8.0.tar.gz",
    "Imports": [
      "igraph",
      "XML",
      "AnnotationDbi"
    ],
    "Suggests": [
      "rgl",
      "impute",
      "DLBCL",
      "genefilter",
      "xtable",
      "ALL",
      "limma",
      "hgu95av2.db"
    ],
    "Package": "BioNet",
    "vignettes": [
      "vignettes/BioNet/inst/doc/cytoscape.pdf",
      "vignettes/BioNet/inst/doc/prec_recall_large.pdf",
      "vignettes/BioNet/inst/doc/prec_recall_small.pdf",
      "vignettes/BioNet/inst/doc/Tutorial-3dplot.pdf",
      "vignettes/BioNet/inst/doc/Tutorial.pdf"
    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "Bioinformatics",
      "DataImport",
      "DifferentialExpression",
      "GeneExpression",
      "GraphsAndNetworks",
      "Microarray",
      "Software",
      "Visualization"
    ],
    "Description": "This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. E.g. p-values obtained from the differential expression of the genes from an Affymetrix array are assigned to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from the p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork.",
    "importsMe": [
      "HTSanalyzeR"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/BioNet_1.8.0.zip"
  },
  "oligoClasses": {
    "Depends": [
      "Biobase (>= 2.7.3)",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/oligoClasses_1.12.2.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/oligoClasses_1.12.2.tgz",
    "Version": "1.12.2",
    "dependsOnMe": [
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      "mBPCR",
      "oligo",
      "pd.081229.hg18.promoter.medip.hx1",
      "pd.2006.07.18.hg18.refseq.promoter",
      "pd.2006.07.18.mm8.refseq.promoter",
      "pd.2006.10.31.rn34.refseq.promoter",
      "pd.charm.hg18.example",
      "pd.cytogenetics.array",
      "pd.feinberg.hg18.me.hx1",
      "pd.feinberg.mm8.me.hx1",
      "pd.genomewidesnp.5",
      "pd.genomewidesnp.6",
      "pd.hg.u95a",
      "pd.hg.u95av2",
      "pd.hg18.60mer.expr",
      "pd.ht.hg.u133.plus.pm",
      "pd.huex.1.0.st.v2",
      "pd.hugene.1.0.st.v1",
      "pd.hugene.1.1.st.v1",
      "pd.mapping250k.nsp",
      "pd.mapping250k.sty",
      "pd.mapping50k.hind240",
      "pd.mapping50k.xba240",
      "pd.moex.1.0.st.v1",
      "pd.mogene.1.0.st.v1",
      "pd.mogene.1.1.st.v1",
      "pd.mouse430.2",
      "pd.raex.1.0.st.v1",
      "pd.ragene.1.0.st.v1",
      "pd.ragene.1.1.st.v1",
      "SNPchip",
      "VanillaICE"
    ],
    "Maintainer": "Benilton Carvalho <carvalho@bclab.org> and Robert Scharpf <rscharpf@jhsph.edu>",
    "Author": "Benilton Carvalho <carvalho@bclab.org> and Robert Scharpf <rscharpf@jhsph.edu>",
    "Title": "Classes for high-throughput arrays supported by oligo",
    "source.ver": "src/contrib/oligoClasses_1.12.2.tar.gz",
    "Imports": [
      "graphics",
      "Biostrings (>= 2.15.11)",
      "affyio (>= 1.15.2)"
    ],
    "Suggests": [
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      "pd.genomewidesnp.5",
      "pd.mapping50k.hind240",
      "pd.mapping50k.xba240",
      "pd.mapping250k.sty",
      "pd.mapping250k.nsp",
      "genomewidesnp6Crlmm",
      "genomewidesnp5Crlmm"
    ],
    "Package": "oligoClasses",
    "License": "GPL (>= 2)",
    "biocViews": [
      "Infrastructure",
      "Software"
    ],
    "Description": "This package contains class definitions, validity checks, and initialization methods for classes used by the oligo and crlmm packages.",
    "Enhances": [
      "ff",
      "snow"
    ],
    "importsMe": [
      "ITALICS",
      "SNPchip"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/oligoClasses_1.12.2.zip"
  },
  "Ruuid": {
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      "R (>= 2.6.0)",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/Ruuid_1.28.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/Ruuid_1.28.0.tgz",
    "Version": "1.28.0",
    "Maintainer": "Biocore Team c/o BioC user list <bioconductor@stat.math.ethz.ch>",
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      "methods"
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    "Author": "Mark Robinson <mrobinson@wehi.edu.au>, Davis McCarthy <dmccarthy@wehi.edu.au>, Gordon Smyth <smyth@wehi.edu.au>",
    "Title": "Empirical analysis of digital gene expression data in R",
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    "Author": "Yang Xie <Yang.Xie@UTSouthwestern.edu>",
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    "Description": "This package provides a model-based background correction method, which incorporates the negative control beads to pre-process Illumina BeadArray data.",
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      "methods"
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    "Author": "Rafael A. Irizarry <rafa@jhu.edu>, Laurent Gautier <laurent@cbs.dtu.dk>, Wolfgang Huber <w.huber@dkfz-heidelberg.de>, Ben Bolstad <bmb@bmbolstad.com>",
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    "Archs": "i386, x64",
    "License": "GPL (>= 2)",
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    "Description": "This package has two functions. One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the location/probe set membership mapping. The other creates a package that automatically loads that environment.",
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    "URL": "http://www-gene.cimr.cam.ac.uk/clayton/software/",
    "Maintainer": "David Clayton <david.clayton@cimr.cam.ac.uk>",
    "Author": "David Clayton <david.clayton@cimr.cam.ac.uk> and Hin-Tak Leung <htl10@users.sourceforge.net>",
    "Title": "The snp.matrix and X.snp.matrix classes",
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    "Suggests": [
      "hexbin"
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    "Package": "snpMatrix",
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    "Description": "Implements classes and methods for large-scale SNP association studies",
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    "URL": "http://www.esat.kuleuven.ac.be/~jallemee,http://www.esat.kuleuven.ac.be/~sdurinck",
    "Maintainer": "Steffen Durinck <steffen@stat.berkeley.edu>",
    "Author": "Steffen Durinck <steffen.durinck@esat.kuleuven.ac.be>, Joke Allemeersch <joke.allemeersch@esat.kuleuven.ac.be> and Vincent Carey <stvjc@channing.harvard.edu>",
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    "biocViews": [
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    "Description": "This package can be used to handle MAGEML documents in Bioconductor"
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    "Description": "A package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since it will extract probe level data using the Affymetrix Power Tools application and wrap these data into a ProbeLevelSet. A ProbeLevelSet directly extends the expressionSet, but includes additional information about the sequence of each probe and the probe set it is derived from. The package includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data.",
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    "Maintainer": "Sjoerd Vosse <info@vossewebdevelopment.nl>",
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    "Title": "Dimension Reduction for Array CGH Data with Minimal Information Loss.",
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    "License": "GPL (http://www.gnu.org/copyleft/gpl.html)",
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    "Description": "High-throughput sequencing technologies allow the production of large volumes of short sequences, which can be aligned to the genome to create a set of matches to the genome. By looking for regions of the genome which to which there are high densities of matches, we can infer a segmentation of the genome into regions of biological significance. The methods in this package allow the simultaneous segmentation of data from multiple samples, taking into account replicate data, in order to create a consensus segmentation. This has obvious applications in a number of classes of sequencing experiments, particularly in the discovery of small RNA loci and novel mRNA transcriptome discovery.",
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      "Biobase (>= 1.4.22)",
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    "Title": "A gene recommender algorithm to identify genes coexpressed with a query set of genes",
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      "stats",
      "graph",
      "hgu95av2.db"
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    "Maintainer": "VJ Carey <stvjc@channing.harvard.edu>",
    "Author": "VJ Carey <stvjc@channing.harvard.edu>",
    "Title": "graph support for KO, KEGG Orthology",
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    "Imports": [
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    "Suggests": [
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    "Package": "keggorthology",
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    "License": "Artistic-2.0",
    "biocViews": [
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      "Software"
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    "Description": "graphical representation of the Feb 2010 KEGG Orthology. The KEGG orthology is a set of pathway IDs that are not to be confused with the KEGG ortholog IDs.",
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    "Version": "1.8.0",
    "URL": "http://bioinfo.curie.fr",
    "Maintainer": "Pierre Gestraud <pierre.gestraud@curie.fr>",
    "Author": "Pierre Gestraud",
    "Title": "Biclustering Analysis and Results Exploration",
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    "Package": "BicARE",
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    "Archs": "i386, x64",
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    "URL": "http://www.biostat.ucsf.edu/jean/",
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    "Author": "Yuanyuan Xiao <yxiao@itsa.ucsf.edu>, Yee Hwa (Jean) Yang <jean@biostat.ucsf.edu>",
    "Title": "Stepwise normalization functions for cDNA microarrays",
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    "Description": "Stepwise normalization functions for cDNA microarray data.",
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/rnaSeqMap_1.0.0.tgz",
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    "Author": "Anna Lesniewska <alesniewska@cs.put.poznan.pl>; Michal Okoniewski <michal@fgcz.ethz.ch>",
    "Title": "rnaSeq analyses using xmapcore database",
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      "IRanges",
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    "License": "GPL-2",
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    "Description": "Provides means of analysis for RNAseq data, used together with genomic annotation from Ensembl. Requires an xmapcore database in MySQL as a back-end, which is also a storage for sequencing reads. Front-end analyses include transformations of the coverage function, splicing analysis, finding irreducible regions with the two-sliding-windows algorithm and genomic region visualizations.",
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      "stats"
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    "Author": "Yann Ruffieux, contributions from Debjani Bhowmick, Anthony C. Davison, and Darlene R. Goldstein",
    "Title": "Laplace Mixture Model in Microarray Experiments",
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    "Imports": [
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    "Maintainer": "H. Pages <hpages@fhcrc.org>",
    "Author": "H. Pages, P. Aboyoun, R. Gentleman, and S. DebRoy",
    "Title": "String objects representing biological sequences, and matching algorithms",
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    "Description": "[ This package has been deprecated. Please use xmapcore instead. ] Provides fine grained annotation of Affymetrix exon arrays, including mappings between the array probes and probesets and the Ensembl exons, transcripts and genes they target.",
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    "Description": "Many functions for computing the NPMLE for censored and truncated data.",
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    "Title": "FDR adjustments of Microarray Experiments (FDR-AME)",
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    "Imports": [
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      "graphics",
      "grDevices",
      "stats",
      "utils"
    ],
    "Package": "fdrame",
    "vignettes": [
      "vignettes/fdrame/inst/doc/fdrame.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL (>= 2)",
    "biocViews": [
      "DifferentialExpression",
      "Microarray",
      "MultipleComparisons",
      "Software"
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    "Description": "This package contains two main functions. The first is fdr.ma which takes normalized expression data array, experimental design and computes adjusted p-values It returns the fdr adjusted p-values and plots, according to the methods described in (Reiner, Yekutieli and Benjamini 2002). The second, is fdr.gui() which creates a simple graphic user interface to access fdr.ma",
    "win.binary.ver": "bin/windows/contrib/2.12/fdrame_1.22.0.zip"
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      "methods",
      "Biobase"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/multtest_2.6.0.zip",
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    "Version": "2.6.0",
    "dependsOnMe": [
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      "ChIPpeakAnno",
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      "KCsmart",
      "LMGene",
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      "siggenes",
      "webbioc"
    ],
    "Maintainer": "Katherine S. Pollard <kpollard@gladstone.ucsf.edu>",
    "Author": "Katherine S. Pollard, Houston N. Gilbert, Yongchao Ge, Sandra Taylor, Sandrine Dudoit",
    "Title": "Resampling-based multiple hypothesis testing",
    "suggestsMe": [
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      "pcot2",
      "safe",
      "SSPA",
      "topGO",
      "xcms"
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    "License": "LGPL",
    "biocViews": [
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    "Description": "Non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR).  Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included.  When probing hypotheses with t-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function.  Results are reported in terms of adjusted p-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments.",
    "importsMe": [
      "ABarray",
      "aCGH",
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      "ChIPpeakAnno",
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      "IsoGeneGUI",
      "OCplus",
      "webbioc"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/multtest_2.6.0.zip"
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      "R (>= 2.11.0)",
      "flowCore",
      "flowViz",
      "flowClust"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/flowTrans_1.2.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/flowTrans_1.2.0.tgz",
    "Version": "1.2.0",
    "Maintainer": "Greg Finak <greg.finak@ircm.qc.ca>",
    "Author": "Greg Finak <greg.finak@ircm.qc.ca>, Juan Manuel-Perez <jperez@ircm.qc.ca>, Raphael Gottardo <raphael.gottardo@ircm.qc.ca>",
    "Title": "Parameter Optimization for Flow Cytometry Data Transformation",
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    "Imports": [
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      "methods",
      "flowViz",
      "stats",
      "flowClust"
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    "Package": "flowTrans",
    "vignettes": [
      "vignettes/flowTrans/inst/doc/flowTrans.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "Bioinformatics",
      "FlowCytometry",
      "Software"
    ],
    "Description": "Profile maximum likelihood estimation of parameters for flow cytometry data transformations.",
    "win.binary.ver": "bin/windows/contrib/2.12/flowTrans_1.2.0.zip"
  },
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    "Depends": [
      "R (>= 2.9.0)",
      "methods",
      "Biobase (>= 2.3.3)"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/affycomp_1.26.0.zip",
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    "Version": "1.26.0",
    "Maintainer": "Rafael A. Irizarry <rafa@jhu.edu>",
    "Author": "Rafael A. Irizarry <rafa@jhu.edu> and Zhijin Wu <zwu@jhsph.edu> with contributions from Simon Cawley <simon_cawley@affymetrix.com>,",
    "Title": "Graphics Toolbox for Assessment of Affymetrix Expression Measures",
    "source.ver": "src/contrib/affycomp_1.26.0.tar.gz",
    "Suggests": [
      "splines"
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    "Package": "affycomp",
    "vignettes": [
      "vignettes/affycomp/inst/doc/affycomp.pdf"
    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "Microarray",
      "OneChannel",
      "Preprocessing",
      "Software"
    ],
    "Description": "The package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays.",
    "win.binary.ver": "bin/windows/contrib/2.12/affycomp_1.26.0.zip"
  },
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    "Depends": [
      "R (>= 2.3.0)",
      "Biobase (>= 1.10.0)",
      "RColorBrewer (>= 0.1-3)",
      "xtable",
      "lattice",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/ddCt_1.4.0.zip",
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    "Version": "1.4.0",
    "Maintainer": "Jitao David Zhang <j.zhang@dkfz.de>",
    "Author": "Jitao David Zhang, Rudolf Biczok and Markus Ruschhaupt",
    "Title": "The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)",
    "source.ver": "src/contrib/ddCt_1.4.0.tar.gz",
    "Package": "ddCt",
    "vignettes": [
      "vignettes/ddCt/inst/doc/RT-PCR-Script-ddCt.pdf",
      "vignettes/ddCt/inst/doc/rtPCR-usage.pdf",
      "vignettes/ddCt/inst/doc/rtPCR.pdf"
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    "biocViews": [
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      "GeneExpression",
      "RT-PCR",
      "Software"
    ],
    "Description": "The Delta-Delta-Ct (ddCt) Algorithm is an approximation method to determine relative gene expression with quantitative real-time PCR (qRT-PCR) experiments. Compared to other approaches, it requires no standard curve for each primer-target pair, therefore reducing the working load and yet returning accurate enough results as long as the assumptions of the amplification efficiency hold. The ddCt package implements a pipeline to collect, analyse and visualize qRT-PCR results, for example those from TaqMan SDM software, mainly using the ddCt method. The pipeline can be either invoked by a script in command-line or through the API consisting of S4-Classes, methods and functions.",
    "win.binary.ver": "bin/windows/contrib/2.12/ddCt_1.4.0.zip"
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      "R (>= 2.10.0)",
      "methods"
    ],
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    "dependsOnMe": [
      "RWebServices"
    ],
    "Maintainer": "Martin Morgan <mtmorgan@fhcrc.org>",
    "Author": "Duncan Temple Lang, John Chambers",
    "Title": "The Omegahat interface for R and Java.",
    "source.ver": "src/contrib/SJava_0.76.0.tar.gz",
    "Package": "SJava",
    "License": "GPL (>= 2)",
    "biocViews": [
      "Infrastructure",
      "Software"
    ],
    "Description": "An interface from R to Java to create and call Java objects and methods."
  },
  "splicegear": {
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      "methods",
      "Biobase(>= 2.5.5)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/splicegear_1.22.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/splicegear_1.22.0.tgz",
    "Version": "1.22.0",
    "Maintainer": "Laurent Gautier <laurent@cbs.dtu.dk>",
    "Author": "Laurent Gautier <laurent@cbs.dtu.dk>",
    "Title": "splicegear",
    "source.ver": "src/contrib/splicegear_1.22.0.tar.gz",
    "Imports": [
      "annotate",
      "Biobase",
      "graphics",
      "grDevices",
      "grid",
      "methods",
      "utils",
      "XML"
    ],
    "Package": "splicegear",
    "vignettes": [
      "vignettes/splicegear/inst/doc/splicegear.pdf"
    ],
    "License": "LGPL",
    "biocViews": [
      "Infrastructure",
      "Software",
      "Transcription"
    ],
    "Description": "A set of tools to work with alternative splicing",
    "win.binary.ver": "bin/windows/contrib/2.12/splicegear_1.22.0.zip"
  },
  "nudge": {
    "win64.binary.ver": "bin/windows64/contrib/2.12/nudge_1.16.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/nudge_1.16.0.tgz",
    "Version": "1.16.0",
    "Maintainer": "N. Dean <nemad@stat.washington.edu>",
    "Author": "N. Dean <nemad@stat.washington.edu> and A. E. Raftery <raftery@stat.washington.edu>",
    "Title": "Normal Uniform Differential Gene Expression detection",
    "source.ver": "src/contrib/nudge_1.16.0.tar.gz",
    "Imports": [
      "stats"
    ],
    "Package": "nudge",
    "vignettes": [
      "vignettes/nudge/inst/doc/nudge.vignette.pdf",
      "vignettes/nudge/inst/doc/nvignplot1.pdf",
      "vignettes/nudge/inst/doc/nvignplot2.pdf",
      "vignettes/nudge/inst/doc/nvignplot3.pdf",
      "vignettes/nudge/inst/doc/nvignplot4.pdf"
    ],
    "License": "GPL",
    "biocViews": [
      "DifferentialExpression",
      "Microarray",
      "Software",
      "TwoChannel"
    ],
    "Description": "Package for normalizing microarray data in single and multiple replicate experiments and fitting a normal-uniform mixture to detect differentially expressed genes in the cases where the two samples are being compared directly or indirectly (via a common reference sample)",
    "win.binary.ver": "bin/windows/contrib/2.12/nudge_1.16.0.zip"
  },
  "GeneR": {
    "Depends": [
      "R (>= 2.6.0)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/GeneR_2.20.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/GeneR_2.20.0.tgz",
    "Version": "2.20.0",
    "dependsOnMe": [
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    ],
    "URL": "http://www.cgm.cnrs-gif.fr",
    "Maintainer": "Y. d'Aubenton-Carafa <daubenton@cgm.cnrs-gif.fr>",
    "Author": "L. Cottret, A. Lucas, E. Marrakchi, O. Rogier, V. Lefort, P. Durosay, A. Viari, C. Thermes & Y. d'Aubenton-Carafa.",
    "Title": "R for genes and sequences analysis",
    "source.ver": "src/contrib/GeneR_2.20.0.tar.gz",
    "Imports": [
      "graphics",
      "stats",
      "utils"
    ],
    "Package": "GeneR",
    "vignettes": [
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      "vignettes/GeneR/inst/doc/GeneR.pdf"
    ],
    "Archs": "i386",
    "License": "CeCILL-2.0",
    "biocViews": [
      "Annotation",
      "Genetics",
      "Software"
    ],
    "Description": "Package manipulating nucleotidic sequences (Embl, Fasta, GenBank)",
    "win.binary.ver": "bin/windows/contrib/2.12/GeneR_2.20.0.zip"
  },
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    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/vsn_3.18.0.zip",
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    "URL": "http://www.r-project.org, http://www.ebi.ac.uk/huber",
    "Maintainer": "Wolfgang Huber <huber@ebi.ac.uk>",
    "Author": "Wolfgang Huber, with contributions from Anja von Heydebreck. Many comments and suggestions by users are acknowledged, among them Dennis Kostka, David Kreil, Hans-Ulrich Klein, Robert Gentleman, Deepayan Sarkar and Gordon Smyth.",
    "Title": "Variance stabilization and calibration for microarray data",
    "suggestsMe": [
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      "BiocCaseStudies",
      "cellHTS",
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    "Package": "vsn",
    "vignettes": [
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    "Archs": "i386, x64",
    "License": "Artistic-2.0",
    "biocViews": [
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      "Preprocessing",
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      "TwoChannel"
    ],
    "Description": "The package implements a method for normalising microarray intensities, both between colours within array, and between arrays. The method uses a robust variant of the maximum-likelihood estimator for the stochastic model of microarray data described in the references (see vignette). The model incorporates data calibration (a.k.a. normalization), a model for the dependence of the variance on the mean intensity, and a variance stabilizing data transformation. Differences between transformed intensities are analogous to \"normalized log-ratios\". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.",
    "importsMe": [
      "imageHTS",
      "Ringo",
      "tilingArray"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/vsn_3.18.0.zip"
  },
  "GeneTraffic": {
    "Depends": [
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      "Biobase (>= 1.4.0)",
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    "win64.binary.ver": "bin/windows64/contrib/2.12/GeneTraffic_1.22.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/GeneTraffic_1.22.0.tgz",
    "Version": "1.22.0",
    "URL": "http://www.iobion.com/web_services/GeneTrafficAPI/",
    "Maintainer": "Daniel Iordan <daniel.iordan@stratagene.com>",
    "Author": "Daniel Iordan <daniel.iordan@stratagene.com>",
    "Title": "GeneTraffic R Integration Functions",
    "source.ver": "src/contrib/GeneTraffic_1.22.0.tar.gz",
    "Imports": [
      "Biobase",
      "digest",
      "marray (>= 1.5.10)",
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      "utils"
    ],
    "Package": "GeneTraffic",
    "vignettes": [
      "vignettes/GeneTraffic/inst/doc/GeneTraffic.pdf"
    ],
    "License": "GPL",
    "biocViews": [
      "Infrastructure",
      "Microarray",
      "Software"
    ],
    "Description": "Set of functions and class definitions to be able to read GeneTraffic specific data from a project summary zip file and covert them to BioConductor objects (for 1 color projects affy's ExpressionSet, for 2 color projects marray's marrayRaw)",
    "win.binary.ver": "bin/windows/contrib/2.12/GeneTraffic_1.22.0.zip"
  },
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    "Depends": [
      "igraph",
      "GSEABase",
      "BioNet",
      "cellHTS2",
      "RankProd",
      "methods"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/HTSanalyzeR_2.3.5.zip",
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    "Version": "2.3.5",
    "Maintainer": "Xin Wang <Xin.Wang@cancer.org.uk>",
    "Author": "Xin Wang <Xin.Wang@cancer.org.uk>, Camille Terfve <cdat2@cam.ac.uk>, John C. Rose <jcr53@cam.ac.uk>, Florian Markowetz <Florian.Markowetz@cancer.org.uk>",
    "Title": "Gene set over-representation, enrichment and network analyses for high-throughput screens",
    "source.ver": "src/contrib/HTSanalyzeR_2.3.5.tar.gz",
    "Imports": [
      "graph",
      "igraph",
      "GSEABase",
      "BioNet",
      "cellHTS2",
      "AnnotationDbi",
      "biomaRt"
    ],
    "Suggests": [
      "KEGG.db",
      "GO.db",
      "org.Dm.eg.db",
      "GOstats",
      "org.Ce.eg.db",
      "org.Mm.eg.db",
      "org.Rn.eg.db",
      "org.Hs.eg.db",
      "snow"
    ],
    "Package": "HTSanalyzeR",
    "vignettes": [
      "vignettes/HTSanalyzeR/inst/doc/Figure.pdf",
      "vignettes/HTSanalyzeR/inst/doc/HTSanalyzeR-Vignette.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "Bioinformatics",
      "CellBasedAssays",
      "MultipleComparisons",
      "Software"
    ],
    "Description": "This package provides classes and methods for gene set over-representation, enrichment and network analyses on high-throughput screens. The over-representation analysis is performed based on hypergeometric tests. The enrichment analysis is based on the GSEA algorithm (Subramanian et al. PNAS 2005). The network analysis identifies enriched subnetworks based on algorithms from the BioNet package (Beisser et al., Bioinformatics 2010). A pipeline is also specifically designed for cellHTS2 object to perform integrative network analyses of high-throughput RNA interference screens. The users can build their own analysis pipeline for their own data set based on this package.",
    "win.binary.ver": "bin/windows/contrib/2.12/HTSanalyzeR_2.3.5.zip"
  },
  "goProfiles": {
    "Depends": [
      "Biobase",
      "AnnotationDbi",
      "GO.db"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/goProfiles_1.12.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/goProfiles_1.12.0.tgz",
    "Version": "1.12.0",
    "Maintainer": "Alex Sanchez <asanchez@ub.edu>",
    "Author": "Alex Sanchez, Jordi Ocana and Miquel Salicru",
    "Title": "goProfiles: an R package for the statistical analysis of functional profiles",
    "source.ver": "src/contrib/goProfiles_1.12.0.tar.gz",
    "Suggests": [
      "org.Hs.eg.db"
    ],
    "Package": "goProfiles",
    "vignettes": [
      "vignettes/goProfiles/inst/doc/goProfiles.pdf"
    ],
    "License": "GPL",
    "biocViews": [
      "GO",
      "Microarray",
      "Software"
    ],
    "Description": "The package implements methods to compare lists of genes based on comparing the corresponding 'functional profiles'.",
    "win.binary.ver": "bin/windows/contrib/2.12/goProfiles_1.12.0.zip"
  },
  "Rmagpie": {
    "Depends": [
      "R (>= 2.6.1)",
      "Biobase (>= 2.5.5)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/Rmagpie_1.6.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/Rmagpie_1.6.0.tgz",
    "Version": "1.6.0",
    "URL": "http://www.bioconductor.org/",
    "Maintainer": "Camille Maumet <Rmagpie@gmail.com>",
    "Author": "Camille Maumet <Rmagpie@gmail.com>, with contributions from C. Ambroise J. Zhu",
    "Title": "MicroArray Gene-expression-based Program In Error rate estimation",
    "source.ver": "src/contrib/Rmagpie_1.6.0.tar.gz",
    "Imports": [
      "Biobase (>= 2.5.5)",
      "e1071",
      "graphics",
      "grDevices",
      "kernlab",
      "methods",
      "pamr",
      "stats",
      "utils"
    ],
    "Suggests": [
      "xtable"
    ],
    "Package": "Rmagpie",
    "vignettes": [
      "vignettes/Rmagpie/inst/doc/Magpie_examples.pdf"
    ],
    "License": "GPL (>= 3)",
    "biocViews": [
      "Classification",
      "Microarray",
      "Software"
    ],
    "Description": "Microarray Classification is designed for both biologists and statisticians. It offers the ability to train a classifier on a labelled microarray dataset and to then use that classifier to predict the class of new observations. A range of modern classifiers are available, including support vector machines (SVMs), nearest shrunken centroids (NSCs)... Advanced methods are provided to estimate the predictive error rate and to report the subset of genes which appear essential in discriminating between classes.",
    "win.binary.ver": "bin/windows/contrib/2.12/Rmagpie_1.6.0.zip"
  },
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      "R (>= 2.6.0)",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/graph_1.28.0.zip",
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    "dependsOnMe": [
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      "GraphAT",
      "GSEABase",
      "hyperdraw",
      "hypergraph",
      "KEGGgraph",
      "keggorthology",
      "maigesPack",
      "nem",
      "ontoTools",
      "pathRender",
      "pkgDepTools",
      "ppiData",
      "RbcBook1",
      "RBGL",
      "RBioinf",
      "RCytoscape",
      "Rgraphviz",
      "RpsiXML",
      "Rredland",
      "Rtreemix",
      "SNAData",
      "SRAdb",
      "topGO",
      "yeastExpData"
    ],
    "Maintainer": "Seth Falcon <sfalcon@fhcrc.org>",
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      "GraphsAndNetworks",
      "Infrastructure",
      "Software"
    ],
    "Description": "tools for working with ontologies and graphs",
    "win.binary.ver": "bin/windows/contrib/2.12/ontoTools_1.28.0.zip"
  },
  "pdInfoBuilder": {
    "Depends": [
      "R (>= 2.11.0)",
      "methods",
      "Biobase (>= 2.5.5)",
      "RSQLite (>= 0.7-1)",
      "affxparser (>= 1.7.3)",
      "oligo (>= 1.9.19)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/pdInfoBuilder_1.14.1.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/pdInfoBuilder_1.14.1.tgz",
    "Version": "1.14.1",
    "Maintainer": "Benilton Carvalho <carvalho@bclab.org>",
    "Author": "Seth Falcon, Benilton Carvalho with contributions by Vince Carey and Matt Settles",
    "Title": "Platform Design Information Package Builder",
    "source.ver": "src/contrib/pdInfoBuilder_1.14.1.tar.gz",
    "Imports": [
      "Biostrings (>= 2.13.50)",
      "IRanges (>= 1.3.89)"
    ],
    "Package": "pdInfoBuilder",
    "vignettes": [
      "vignettes/pdInfoBuilder/inst/doc/BuildingPDInfoPkgs.pdf",
      "vignettes/pdInfoBuilder/inst/doc/howto-AffymetrixMapping.pdf"
    ],
    "Archs": "i386, x64",
    "License": "Artistic-2.0",
    "biocViews": [
      "Annotation",
      "Infrastructure",
      "Software"
    ],
    "Description": "Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg.",
    "win.binary.ver": "bin/windows/contrib/2.12/pdInfoBuilder_1.14.1.zip"
  },
  "domainsignatures": {
    "Depends": [
      "R (>= 2.4.0)",
      "KEGG.db",
      "prada",
      "biomaRt",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/domainsignatures_1.10.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/domainsignatures_1.10.0.tgz",
    "Version": "1.10.0",
    "Maintainer": "Florian Hahne <florian.hahne@novartis.com>",
    "Author": "Florian Hahne, Tim Beissbarth",
    "Title": "Geneset enrichment based on InterPro domain signatures",
    "source.ver": "src/contrib/domainsignatures_1.10.0.tar.gz",
    "Imports": [
      "AnnotationDbi"
    ],
    "Package": "domainsignatures",
    "vignettes": [
      "vignettes/domainsignatures/inst/doc/domainenrichment.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "Annotation",
      "Bioinformatics",
      "Pathways",
      "Software"
    ],
    "Description": "Find significantly enriched gene classifications in a list of functionally undescribed genes based on their InterPro domain structure.",
    "win.binary.ver": "bin/windows/contrib/2.12/domainsignatures_1.10.0.zip"
  },
  "Agi4x44PreProcess": {
    "Depends": [
      "R (>= 2.6.0)",
      "Biobase",
      "limma",
      "annotate",
      "genefilter"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/Agi4x44PreProcess_1.10.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/Agi4x44PreProcess_1.10.0.tgz",
    "Version": "1.10.0",
    "Maintainer": "Pedro Lopez-Romero <plopez@cnic.es>",
    "Author": "Pedro Lopez-Romero <plopez@cnic.es>",
    "Title": "PreProcessing of Agilent 4x44 array data",
    "source.ver": "src/contrib/Agi4x44PreProcess_1.10.0.tar.gz",
    "Suggests": [
      "vsn",
      "affycoretools",
      "hgug4112a.db",
      "GO.db",
      "marray",
      "gplots",
      "gtools",
      "gdata"
    ],
    "Package": "Agi4x44PreProcess",
    "vignettes": [
      "vignettes/Agi4x44PreProcess/inst/doc/Agi4x44PreProcess.pdf"
    ],
    "License": "GPL-3",
    "biocViews": [
      "Agilent",
      "Microarray",
      "OneChannel",
      "Preprocessing",
      "Software"
    ],
    "Description": "Preprocessing of Agilent 4x44 array data",
    "win.binary.ver": "bin/windows/contrib/2.12/Agi4x44PreProcess_1.10.0.zip"
  },
  "Mfuzz": {
    "Depends": [
      "R (>= 2.5.0)",
      "Biobase (>= 2.5.5)",
      "e1071"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/Mfuzz_2.8.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/Mfuzz_2.8.0.tgz",
    "Version": "2.8.0",
    "dependsOnMe": [
      "cycle"
    ],
    "URL": "http://www.sysbiolab.eu",
    "Maintainer": "Matthias Futschik <mfutschik@ualg.pt>",
    "Author": "Matthias Futschik <mfutschik@ualg.pt>",
    "Title": "Soft clustering of time series gene expression data",
    "source.ver": "src/contrib/Mfuzz_2.8.0.tar.gz",
    "Imports": [
      "tcltk",
      "tkWidgets"
    ],
    "Suggests": [
      "marray"
    ],
    "Package": "Mfuzz",
    "vignettes": [
      "vignettes/Mfuzz/inst/doc/Mfuzz.pdf",
      "vignettes/Mfuzz/inst/doc/MfuzzguiScreenshot.pdf",
      "vignettes/Mfuzz/inst/doc/yeasttable3.pdf"
    ],
    "License": "GPL-2",
    "biocViews": [
      "Clustering",
      "Microarray",
      "Preprocessing",
      "Software",
      "TimeCourse",
      "Visualization"
    ],
    "Description": "Package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)",
    "importsMe": [
      "maSigPro"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/Mfuzz_2.8.0.zip"
  },
  "affyPara": {
    "Depends": [
      "R (>= 2.5.0)",
      "methods",
      "affy (>= 1.20.0)",
      "snow (>= 0.2-3)",
      "vsn (>= 3.6.0)",
      "aplpack (>= 1.1.1)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/affyPara_1.10.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/affyPara_1.10.0.tgz",
    "Version": "1.10.0",
    "URL": "http://www.ibe.med.uni-muenchen.de",
    "Maintainer": "Markus Schmidberger <schmidberger@rostlab.org>",
    "Author": "Markus Schmidberger <schmidb@ibe.med.uni-muenchen.de>, Esmeralda Vicedo <e.vicedo@gmx.net>, Ulrich Mansmann <mansmann@ibe.med.uni-muenchen.de>",
    "Title": "Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays",
    "source.ver": "src/contrib/affyPara_1.10.0.tar.gz",
    "Suggests": [
      "affydata"
    ],
    "Package": "affyPara",
    "vignettes": [
      "vignettes/affyPara/inst/doc/affyPara.pdf",
      "vignettes/affyPara/inst/doc/vsnStudy.pdf"
    ],
    "License": "GPL-3",
    "biocViews": [
      "Microarray",
      "Preprocessing",
      "Software"
    ],
    "Description": "The package contains parallelized functions for exploratory oligonucleotide array analysis. The package is designed for large numbers of microarray data.",
    "Enhances": [
      "affy"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/affyPara_1.10.0.zip"
  },
  "GenomeGraphs": {
    "Depends": [
      "methods",
      "biomaRt",
      "grid"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/GenomeGraphs_1.10.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/GenomeGraphs_1.10.0.tgz",
    "Version": "1.10.0",
    "dependsOnMe": [
      "Genominator"
    ],
    "Maintainer": "Steffen Durinck <sdurinck@lbl.gov>",
    "Author": "Steffen Durinck <sdurinck@lbl.gov>, James Bullard <bullard@berkeley.edu>",
    "Title": "Plotting genomic information from Ensembl",
    "suggestsMe": [
      "leeBamViews",
      "oneChannelGUI",
      "rMAT"
    ],
    "source.ver": "src/contrib/GenomeGraphs_1.10.0.tar.gz",
    "Package": "GenomeGraphs",
    "vignettes": [
      "vignettes/GenomeGraphs/inst/doc/GenomeGraphs.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "Microarray",
      "Software",
      "Visualization"
    ],
    "Description": "Genomic data analyses requires integrated visualization of known genomic information and new experimental data. GenomeGraphs uses the biomaRt package to perform live annotation queries to Ensembl and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.  Another strength of GenomeGraphs is to plot different data types such as array CGH, gene expression, sequencing and other data, together in one plot using the same genome coordinate system.",
    "win.binary.ver": "bin/windows/contrib/2.12/GenomeGraphs_1.10.0.zip"
  },
  "tigre": {
    "Depends": [
      "R (>= 2.11.0)",
      "Biobase"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/tigre_1.4.2.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/tigre_1.4.2.tgz",
    "Version": "1.4.2",
    "URL": "http://www.bioinf.manchester.ac.uk/resources/tiger/",
    "Maintainer": "Antti Honkela <antti.honkela@hiit.fi>",
    "Author": "Antti Honkela, Pei Gao, Jonatan Ropponen, Miika-Petteri Matikainen, Magnus Rattray, Neil D. Lawrence",
    "Title": "Transcription factor Inference through Gaussian process Reconstruction of Expression",
    "source.ver": "src/contrib/tigre_1.4.2.tar.gz",
    "Imports": [
      "Biobase",
      "methods",
      "AnnotationDbi",
      "gplots",
      "graphics",
      "puma",
      "stats",
      "utils",
      "annotate",
      "DBI",
      "RSQLite"
    ],
    "Suggests": [
      "puma",
      "drosgenome1.db",
      "annotate"
    ],
    "Package": "tigre",
    "vignettes": [
      "vignettes/tigre/inst/doc/tigre_quick.pdf",
      "vignettes/tigre/inst/doc/tigre-009.pdf",
      "vignettes/tigre/inst/doc/tigre-010.pdf",
      "vignettes/tigre/inst/doc/tigre-011.pdf",
      "vignettes/tigre/inst/doc/tigre.pdf"
    ],
    "Archs": "i386, x64",
    "License": "AGPL-3",
    "biocViews": [
      "Bioinformatics",
      "GeneExpression",
      "Microarray",
      "Software",
      "TimeCourse",
      "Transcription"
    ],
    "Description": "The tigre package implements our methodology of Gaussian process differential equation models for analysis of gene expression time series from single input motif networks. The package can be used for inferring unobserved transcription factor (TF) protein concentrations from expression measurements of known target genes, or for ranking candidate targets of a TF.",
    "win.binary.ver": "bin/windows/contrib/2.12/tigre_1.4.2.zip"
  },
  "maanova": {
    "Depends": [
      "R (>= 2.7.0)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/maanova_1.20.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/maanova_1.20.0.tgz",
    "Version": "1.20.0",
    "URL": "http://research.jax.org/faculty/churchill",
    "Maintainer": "Keith Sheppard <keith.sheppard@jax.org>",
    "Author": "Hao Wu, modified by Hyuna Yang and Keith Sheppard with ideas from Gary Churchill, Katie Kerr and Xiangqin Cui.",
    "Title": "Tools for analyzing Micro Array experiments",
    "source.ver": "src/contrib/maanova_1.20.0.tar.gz",
    "Imports": [
      "Biobase",
      "graphics",
      "grDevices",
      "methods",
      "stats",
      "utils"
    ],
    "Suggests": [
      "qvalue",
      "snow"
    ],
    "Package": "maanova",
    "vignettes": [
      "vignettes/maanova/inst/doc/abf1fig.pdf",
      "vignettes/maanova/inst/doc/hckidney.pdf",
      "vignettes/maanova/inst/doc/maanova.pdf",
      "vignettes/maanova/inst/doc/vgprofile.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL (>= 2)",
    "biocViews": [
      "Clustering",
      "DifferentialExpression",
      "Microarray",
      "Software"
    ],
    "Description": "Analysis of N-dye Micro Array experiment using mixed model effect. Containing analysis of variance, permutation and bootstrap, cluster and consensus tree.",
    "Enhances": [
      "Rmpi"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/maanova_1.20.0.zip"
  },
  "Mulcom": {
    "Depends": [
      "R (>= 2.11.1)",
      "fields",
      "Biobase"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/Mulcom_1.0.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/Mulcom_1.0.0.tgz",
    "Version": "1.0.0",
    "Maintainer": "Claudio Isella <claudio.isella@ircc.it>",
    "Author": "Claudio Isella",
    "Title": "Calculates MulCom test",
    "source.ver": "src/contrib/Mulcom_1.0.0.tar.gz",
    "Imports": [
      "graphics",
      "grDevices",
      "stats",
      "methods"
    ],
    "Package": "Mulcom",
    "vignettes": [
      "vignettes/Mulcom/inst/doc/MulcomVignette.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL-2",
    "biocViews": [
      "DifferentialExpression",
      "GeneExpression",
      "Microarray",
      "MultipleComparisons",
      "Software",
      "Statistics"
    ],
    "Description": "Identification of differentially expressed genes and false discovery rate (FDR) calculation by Multiple Comparison test",
    "win.binary.ver": "bin/windows/contrib/2.12/Mulcom_1.0.0.zip"
  },
  "genArise": {
    "Depends": [
      "R (>= 1.7.1)",
      "locfit",
      "tkrplot",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/genArise_1.26.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/genArise_1.26.0.tgz",
    "Version": "1.26.0",
    "URL": "http://www.ifc.unam.mx/genarise",
    "Maintainer": "IFC Development Team <info-genarise@ifc.unam.mx>",
    "Author": "Ana Patricia Gomez Mayen <pgomez@ifc.unam.mx>,\\\\ Gustavo Corral Guille <gcorral@ifc.unam.mx>, \\\\ Lina Riego Ruiz <lriego@ifc.unam.mx>,\\\\ Gerardo Coello Coutino <gcoello@ifc.unam.mx>",
    "Title": "Microarray Analysis tool",
    "source.ver": "src/contrib/genArise_1.26.0.tar.gz",
    "Imports": [
      "graphics",
      "grDevices",
      "methods",
      "stats",
      "tcltk",
      "utils",
      "xtable"
    ],
    "Package": "genArise",
    "vignettes": [
      "vignettes/genArise/inst/doc/genArise.pdf"
    ],
    "License": "file LICENSE",
    "biocViews": [
      "Microarray",
      "Preprocessing",
      "Software",
      "TwoChannel"
    ],
    "Description": "genArise is an easy to use tool for dual color microarray data. Its GUI-Tk based environment let any non-experienced user performs a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer.",
    "win.binary.ver": "bin/windows/contrib/2.12/genArise_1.26.0.zip"
  },
  "Rgraphviz": {
    "Depends": [
      "R (>= 2.6.0)",
      "methods",
      "utils",
      "graph",
      "grid"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/Rgraphviz_1.28.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/Rgraphviz_1.28.0.tgz",
    "Version": "1.28.0",
    "dependsOnMe": [
      "biocGraph",
      "BioMVCClass",
      "hyperdraw",
      "KEGGgraph",
      "nem",
      "pathRender"
    ],
    "Maintainer": "Kasper Hansen <khansen@stat.berkeley.edu>",
    "Author": "Jeff Gentry <jgentry@jimmy.harvard.edu>, Li Long <li.long@isb-sib.ch>, Robert Gentleman <rgentlem@fhcrc.org>, Seth Falcon <sfalcon@fhcrc.org>, Florian Hahne <fhahne@fhcrc.org>, Deepayan Sarkar <dsarkar@fhcrc.org>, Kasper Hansen <khansen@stat.berkeley.edu>",
    "Title": "Provides plotting capabilities for R graph objects",
    "suggestsMe": [
      "altcdfenvs",
      "BiocCaseStudies",
      "Category",
      "DEGraph",
      "flowCore",
      "geneplotter",
      "globaltest",
      "GOstats",
      "oneChannelGUI",
      "pkgDepTools",
      "RBGL",
      "RpsiXML",
      "Rtreemix",
      "safe",
      "SNAData",
      "SPIA",
      "SRAdb",
      "topGO"
    ],
    "source.ver": "src/contrib/Rgraphviz_1.28.0.tar.gz",
    "Imports": [
      "graph",
      "graphics",
      "grDevices",
      "grid",
      "methods",
      "utils"
    ],
    "Package": "Rgraphviz",
    "vignettes": [
      "vignettes/Rgraphviz/inst/doc/newRgraphvizInterface.pdf",
      "vignettes/Rgraphviz/inst/doc/Rgraphviz.pdf"
    ],
    "Archs": "i386",
    "License": "Artistic-2.0",
    "biocViews": [
      "GraphsAndNetworks",
      "Software"
    ],
    "Description": "Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package. Users on all platforms must install graphviz; see the README file, available in the source distribution of this file, for details.",
    "SystemRequirements": "Graphviz version >= 2.2",
    "importsMe": [
      "apComplex",
      "biocGraph",
      "DEGraph",
      "GeneAnswers",
      "nem"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/Rgraphviz_1.28.0.zip"
  },
  "ChIPpeakAnno": {
    "Depends": [
      "biomaRt",
      "multtest",
      "IRanges",
      "Biostrings",
      "BSgenome",
      "BSgenome.Ecoli.NCBI.20080805",
      "GO.db",
      "org.Hs.eg.db",
      "limma"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/ChIPpeakAnno_1.6.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/ChIPpeakAnno_1.6.0.tgz",
    "Version": "1.6.0",
    "Maintainer": "Lihua Julie Zhu <julie.zhu@umassmed.edu>",
    "Author": "Lihua Julie Zhu, Herve Pages, Claude Gazin, Nathan Lawson,Simon Lin, David Lapointe and Michael Green",
    "Title": "Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments.",
    "suggestsMe": [
      "oneChannelGUI"
    ],
    "source.ver": "src/contrib/ChIPpeakAnno_1.6.0.tar.gz",
    "Imports": [
      "biomaRt",
      "multtest",
      "IRanges",
      "Biostrings",
      "BSgenome",
      "GO.db",
      "limma"
    ],
    "Package": "ChIPpeakAnno",
    "vignettes": [
      "vignettes/ChIPpeakAnno/inst/doc/ChIPpeakAnno.pdf"
    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "Annotation",
      "ChIPchip",
      "ChIPseq",
      "Software"
    ],
    "Description": "The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. This package leverages the biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest and stat packages",
    "win.binary.ver": "bin/windows/contrib/2.12/ChIPpeakAnno_1.6.0.zip"
  },
  "maigesPack": {
    "Depends": [
      "R (>= 2.0.0)",
      "convert",
      "graph",
      "limma",
      "marray",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/maigesPack_1.14.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/maigesPack_1.14.0.tgz",
    "Version": "1.14.0",
    "URL": "http://www.maiges.org/en/software/",
    "Maintainer": "Gustavo H. Esteves <gesteves@gmail.com>",
    "Author": "Gustavo H. Esteves <gesteves@gmail.com>, with contributions from Roberto Hirata Jr <hirata@ime.usp.br>, E. Jordao Neves <neves@ime.usp.br>, Elier B. Cristo <elier@ime.usp.br>, Ana C. Simoes <anakqui@ime.usp.br> and Lucas Fahham <fahham@linux.ime.usp.br>",
    "Title": "Functions to handle cDNA microarray data, including several methods of data analysis",
    "source.ver": "src/contrib/maigesPack_1.14.0.tar.gz",
    "Suggests": [
      "amap",
      "annotate",
      "class",
      "e1071",
      "MASS",
      "multtest",
      "OLIN",
      "R2HTML",
      "rgl",
      "som"
    ],
    "Package": "maigesPack",
    "vignettes": [
      "vignettes/maigesPack/inst/doc/maigesPack_tutorial.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL (>= 2)",
    "biocViews": [
      "Bioinformatics",
      "Classification",
      "Clustering",
      "DifferentialExpression",
      "GraphsAndNetworks",
      "Microarray",
      "Preprocessing",
      "Software",
      "TwoChannel"
    ],
    "Description": "This package uses functions of various other packages together with other functions in a coordinated way to handle and analyse cDNA microarray data",
    "win.binary.ver": "bin/windows/contrib/2.12/maigesPack_1.14.0.zip"
  },
  "snapCGH": {
    "Depends": [
      "limma",
      "DNAcopy",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/snapCGH_1.20.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/snapCGH_1.20.0.tgz",
    "Version": "1.20.0",
    "dependsOnMe": [
      "ADaCGH2"
    ],
    "Maintainer": "John Marioni <marioni@uchicago.edu>",
    "Author": "Mike L. Smith, John C. Marioni, Steven McKinney, Thomas Hardcastle, Natalie P. Thorne",
    "Title": "Segmentation, normalisation and processing of aCGH data.",
    "suggestsMe": [
      "beadarraySNP"
    ],
    "source.ver": "src/contrib/snapCGH_1.20.0.tar.gz",
    "Imports": [
      "aCGH",
      "cluster",
      "DNAcopy",
      "GLAD",
      "graphics",
      "grDevices",
      "limma",
      "methods",
      "stats",
      "tilingArray",
      "utils"
    ],
    "Package": "snapCGH",
    "vignettes": [
      "vignettes/snapCGH/inst/doc/snapCGHguide.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL",
    "biocViews": [
      "CopyNumberVariants",
      "Microarray",
      "Preprocessing",
      "Software",
      "TwoChannel"
    ],
    "Description": "Methods for segmenting, normalising and processing aCGH data; including plotting functions for visualising raw and segmented data for individual and multiple arrays.",
    "win.binary.ver": "bin/windows/contrib/2.12/snapCGH_1.20.0.zip"
  },
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    "Depends": [
      "R (>= 2.5)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/vbmp_1.18.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/vbmp_1.18.0.tgz",
    "Version": "1.18.0",
    "URL": "http://bioinformatics.oxfordjournals.org/cgi/content/short/btm535v1",
    "Maintainer": "Nicola Lama <nicola.lama@unina2.it>",
    "Author": "Nicola Lama <nicola.lama@unina2.it>, Mark Girolami <girolami@dcs.gla.ac.uk>",
    "Title": "Variational Bayesian Multinomial Probit Regression",
    "source.ver": "src/contrib/vbmp_1.18.0.tar.gz",
    "Suggests": [
      "Biobase (>= 2.5.5)",
      "statmod"
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    "Package": "vbmp",
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      "vignettes/vbmp/inst/doc/vbmp.pdf"
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    "License": "GPL (>= 2)",
    "biocViews": [
      "Bioinformatics",
      "Classification",
      "Software"
    ],
    "Description": "Variational Bayesian Multinomial Probit Regression with Gaussian Process Priors. It estimates class membership posterior probability employing variational and sparse approximation to the full posterior. This software also incorporates feature weighting by means of Automatic Relevance Determination.",
    "win.binary.ver": "bin/windows/contrib/2.12/vbmp_1.18.0.zip"
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    "Depends": [
      "LogicReg"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/logicFS_1.20.0.zip",
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    "Version": "1.20.0",
    "Maintainer": "Holger Schwender <holger.schw@gmx.de>",
    "Author": "Holger Schwender",
    "Title": "Identification of SNP Interactions",
    "source.ver": "src/contrib/logicFS_1.20.0.tar.gz",
    "Suggests": [
      "genefilter",
      "siggenes"
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    "Package": "logicFS",
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      "vignettes/logicFS/inst/doc/logicFS.pdf"
    ],
    "License": "LGPL (>= 2)",
    "biocViews": [
      "Classification",
      "FeatureSelection",
      "Genetics",
      "SNP",
      "Software"
    ],
    "Description": "Identification of interactions between binary variables using Logic Regression. Can, e.g., be used to find interesting SNP interactions. Contains also a bagging version of logic regression for classification.",
    "win.binary.ver": "bin/windows/contrib/2.12/logicFS_1.20.0.zip"
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    "Version": "1.2.3",
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      "ind1KG",
      "leeBamViews",
      "ShortRead"
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    "URL": "http://bioconductor.org/packages/release/bioc/html/Rsamtools.html",
    "Maintainer": "Biocore Team c/o BioC user list <bioconductor@stat.math.ethz.ch>",
    "Author": "Martin Morgan, Herv\\'e Pag\\`es",
    "Title": "Import aligned BAM file format sequences into R / Bioconductor",
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      "R453Plus1Toolbox"
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      "utils",
      "IRanges",
      "GenomicRanges",
      "Biostrings"
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    "Suggests": [
      "ShortRead",
      "GenomicFeatures",
      "RUnit",
      "KEGG.db"
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    "Package": "Rsamtools",
    "vignettes": [
      "vignettes/Rsamtools/inst/doc/Rsamtools-Overview.pdf"
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    "Archs": "i386, x64",
    "License": "Artistic-2.0",
    "LinkingTo": "Biostrings, IRanges",
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      "DataImport",
      "HighThroughputSequencing",
      "Sequencing",
      "Software"
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    "Description": "This package provides an interface to the 'samtools' utilities for manipulating SAM (Sequence Alignment / Map) format files. Facilities currently available include flexible file input.",
    "importsMe": [
      "R453Plus1Toolbox",
      "ShortRead"
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    "win.binary.ver": "bin/windows/contrib/2.12/Rsamtools_1.2.3.zip"
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  "flowUtils": {
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      "R (>= 2.2.0)",
      "flowCore (>= 1.2.0)"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/flowUtils_1.10.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/flowUtils_1.10.0.tgz",
    "Version": "1.10.0",
    "Maintainer": "Nishant Gopalakrishnan <ngopalak@fhcrc.org>",
    "Author": "Gopalakrishnan N, F. Hahne, B. Ellis, R. Gentleman M. Dalphin,N. Le Meur, B. Purcell.",
    "Title": "Utilities for flow cytometry",
    "suggestsMe": [
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    "source.ver": "src/contrib/flowUtils_1.10.0.tar.gz",
    "Imports": [
      "Biobase",
      "flowCore",
      "graph",
      "methods",
      "RUnit",
      "stats",
      "utils",
      "XML",
      "flowViz"
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    "Suggests": [
      "gatingMLData"
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    "Package": "flowUtils",
    "License": "Artistic-2.0",
    "biocViews": [
      "CellBasedAssays",
      "Flowcytometry",
      "Infrastructure",
      "Software"
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    "Description": "Provides utilities for flow cytometry data.",
    "win.binary.ver": "bin/windows/contrib/2.12/flowUtils_1.10.0.zip"
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    "Depends": [
      "R (>= 2.8.0)",
      "intervals (>= 0.12.2)",
      "Biobase",
      "methods"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/genomeIntervals_1.6.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/genomeIntervals_1.6.0.tgz",
    "Version": "1.6.0",
    "dependsOnMe": [
      "girafe"
    ],
    "Maintainer": "Julien Gagneur <gagneur@embl.de>",
    "Author": "Julien Gagneur <gagneur@embl.de>, Richard Bourgon",
    "Title": "Operations on genomic intervals",
    "source.ver": "src/contrib/genomeIntervals_1.6.0.tar.gz",
    "Package": "genomeIntervals",
    "vignettes": [
      "vignettes/genomeIntervals/inst/doc/genomeIntervals.pdf"
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    "License": "Artistic-2.0",
    "biocViews": [
      "DataImport",
      "Genetics",
      "Infrastructure",
      "Software"
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    "Description": "Tools for operation on genomic intervals.",
    "win.binary.ver": "bin/windows/contrib/2.12/genomeIntervals_1.6.0.zip"
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  "SRAdb": {
    "Depends": [
      "RSQLite (>= 0.8-4)",
      "graph"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/SRAdb_1.4.1.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/SRAdb_1.4.1.tgz",
    "Version": "1.4.1",
    "URL": "http://watson.nci.nih.gov/",
    "Maintainer": "Jack Zhu <zhujack@mail.nih.gov>",
    "Author": "Jack Zhu and Sean Davis",
    "Title": "A compilation of metadata from NCBI SRA and tools",
    "source.ver": "src/contrib/SRAdb_1.4.1.tar.gz",
    "Imports": [
      "RCurl",
      "GEOquery"
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    "Suggests": [
      "Rgraphviz"
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    "Package": "SRAdb",
    "vignettes": [
      "vignettes/SRAdb/inst/doc/SRAdb.pdf"
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    "License": "Artistic-2.0",
    "biocViews": [
      "DataImport",
      "HighThroughputSequencing",
      "Infrastructure",
      "Software"
    ],
    "Description": "The Sequence Read Archive (SRA) is the largest public repository of sequencing data from the next generation of sequencing platforms including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, and others. However, finding data of interest can be challenging using current tools. SRAdb is an attempt to make access to the metadata associated with submission, study, sample, experiment and run much more feasible. This is accomplished by parsing all the NCBI SRA metadata into a SQLite database that can be stored and queried locally. Fulltext search in the package make querying metadata very flexible and powerful.  SRA data files (sra or sra-lite) can be downloaded for doing alignment locally. The SQLite database is updated regularly as new data is added to SRA and can be downloaded at will for the most up-to-date metadata.",
    "win.binary.ver": "bin/windows/contrib/2.12/SRAdb_1.4.1.zip"
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  "KEGGgraph": {
    "Depends": [
      "methods",
      "XML (>= 2.3-0)",
      "graph",
      "Rgraphviz (>= 1.22.0)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/KEGGgraph_1.6.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/KEGGgraph_1.6.0.tgz",
    "Version": "1.6.0",
    "URL": "http://www.dkfz.de/en/mga/index.html",
    "Maintainer": "Jitao David Zhang <j.zhang@dkfz.de>",
    "Author": "Jitao David Zhang and Stefan Wiemann",
    "Title": "KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor",
    "suggestsMe": [
      "DEGraph",
      "SPIA"
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    "source.ver": "src/contrib/KEGGgraph_1.6.0.tar.gz",
    "Imports": [
      "methods",
      "XML",
      "graph"
    ],
    "Suggests": [
      "RBGL",
      "KEGG.db",
      "org.Hs.eg.db",
      "hgu133plus2.db",
      "SPIA"
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    "Package": "KEGGgraph",
    "vignettes": [
      "vignettes/KEGGgraph/inst/doc/KEGGgraph.pdf",
      "vignettes/KEGGgraph/inst/doc/KEGGgraphApp.pdf"
    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "GraphsAndNetworks",
      "Pathways",
      "Software"
    ],
    "Description": "KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.",
    "importsMe": [
      "DEGraph"
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    "win.binary.ver": "bin/windows/contrib/2.12/KEGGgraph_1.6.0.zip"
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  "imageHTS": {
    "Depends": [
      "R (>= 2.9.0)",
      "EBImage (>= 3.2.0)",
      "cellHTS2 (>= 2.10.0)"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/imageHTS_1.0.0.zip",
    "Version": "1.0.0",
    "Maintainer": "Gregoire Pau <gregoire.pau@embl.de>",
    "Author": "Gregoire Pau, Xian Zhang, Michael Boutros, Wolfgang Huber",
    "Title": "Analysis of high-throughput microscopy-based screens",
    "source.ver": "src/contrib/imageHTS_1.0.0.tar.gz",
    "Imports": [
      "tools",
      "Biobase",
      "hwriter",
      "methods",
      "vsn",
      "stats",
      "utils",
      "e1071"
    ],
    "Package": "imageHTS",
    "vignettes": [
      "vignettes/imageHTS/inst/doc/imageHTS-introduction.pdf"
    ],
    "License": "LGPL-2.1",
    "biocViews": [
      "CellBasedAssays",
      "Preprocessing",
      "Software",
      "Visualization"
    ],
    "Description": "imageHTS is an R package dedicated to the analysis of high-throughput microscopy-based screens. The package provides a modular and extensible framework to segment cells, extract quantitative cell features, predict cell types and browse screen data through web interfaces. Designed to operate in distributed environments, imageHTS provides a standardized access to remote screen data, facilitating the dissemination of high-throughput microscopy-based screens.",
    "win.binary.ver": "bin/windows/contrib/2.12/imageHTS_1.0.0.zip"
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  "chipseq": {
    "Depends": [
      "methods",
      "IRanges (>= 1.7.13)",
      "GenomicRanges (>= 1.1.29)",
      "BSgenome",
      "ShortRead"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/chipseq_1.0.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/chipseq_1.0.0.tgz",
    "Version": "1.0.0",
    "Maintainer": "Biocore Team c/o BioC user list <bioconductor@stat.math.ethz.ch>",
    "Author": "Deepayan Sarkar, Robert Gentleman, Michael Lawrence, Zizhen Yao",
    "Title": "chipseq: A package for analyzing chipseq data",
    "suggestsMe": [
      "oneChannelGUI"
    ],
    "source.ver": "src/contrib/chipseq_1.0.0.tar.gz",
    "Imports": [
      "BSgenome",
      "GenomicRanges",
      "IRanges",
      "lattice",
      "methods",
      "ShortRead",
      "stats"
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    "Suggests": [
      "GenomicFeatures",
      "BSgenome.Mmusculus.UCSC.mm9"
    ],
    "Package": "chipseq",
    "vignettes": [
      "vignettes/chipseq/inst/doc/Workflow.pdf"
    ],
    "Archs": "i386, x64",
    "License": "Artistic-2.0",
    "biocViews": [
      "ChIPseq",
      "Software"
    ],
    "Description": "Tools for helping process short read data for chipseq experiments",
    "win.binary.ver": "bin/windows/contrib/2.12/chipseq_1.0.0.zip"
  },
  "flowFlowJo": {
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      "R (>= 2.5.0)",
      "MASS"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/flowFlowJo_1.8.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/flowFlowJo_1.8.0.tgz",
    "Version": "1.8.0",
    "Maintainer": "John J. Gosink <gosinkj@amgen.com>",
    "Author": "John J. Gosink <gosinkj@amgen.com>",
    "Title": "Tools for extracting information from a FlowJo workspace and working with the data in the flowCore paradigm.",
    "source.ver": "src/contrib/flowFlowJo_1.8.0.tar.gz",
    "Imports": [
      "flowCore",
      "XML (>= 1.96)",
      "methods",
      "Biobase"
    ],
    "Package": "flowFlowJo",
    "vignettes": [
      "vignettes/flowFlowJo/inst/doc/flowFlowJo.pdf"
    ],
    "License": "GPL (>=3)",
    "biocViews": [
      "FlowCytometry",
      "Software"
    ],
    "Description": "FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data.  One of the FlowJo standard export file types is the \"FlowJo Workspace\".  This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment.  This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm.",
    "win.binary.ver": "bin/windows/contrib/2.12/flowFlowJo_1.8.0.zip"
  },
  "girafe": {
    "Depends": [
      "R (>= 2.10.0)",
      "methods",
      "IRanges (>= 1.3.53)",
      "Rsamtools",
      "ShortRead (>= 1.3.21)",
      "intervals (>= 0.13.1)",
      "genomeIntervals (>= 1.1.1)",
      "grid"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/girafe_1.2.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/girafe_1.2.0.tgz",
    "Version": "1.2.0",
    "dependsOnMe": [
      "oneChannelGUI"
    ],
    "Maintainer": "J. Toedling <joern.toedling@curie.fr>",
    "Author": "Joern Toedling, Wolfgang Huber",
    "Title": "Genome Intervals and Read Alignments for Functional Exploration",
    "source.ver": "src/contrib/girafe_1.2.0.tar.gz",
    "Imports": [
      "methods",
      "Biobase",
      "Biostrings",
      "BSgenome",
      "graphics",
      "grDevices",
      "stats",
      "utils"
    ],
    "Suggests": [
      "MASS",
      "org.Mm.eg.db",
      "RColorBrewer"
    ],
    "Package": "girafe",
    "vignettes": [
      "vignettes/girafe/inst/doc/girafe.pdf",
      "vignettes/girafe/inst/doc/Rplots.pdf"
    ],
    "Archs": "i386, x64",
    "License": "Artistic-2.0",
    "biocViews": [
      "HighThroughputSequencing",
      "Sequencing",
      "Software"
    ],
    "Description": "The package 'girafe' deals with the genome-level representation of aligned reads from next-generation sequencing data. It contains an object class for enabling a detailed description of genome intervals with aligned reads and functions for comparing, visualising, exporting and working with such intervals and the aligned reads. As such, the package interacts with and provides a link between the packages ShortRead, IRanges and genomeIntervals.",
    "Enhances": [
      "genomeIntervals"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/girafe_1.2.0.zip"
  },
  "netresponse": {
    "Depends": [
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/netresponse_1.0.2.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/netresponse_1.0.2.tgz",
    "Version": "1.0.2",
    "URL": "http://netpro.r-forge.r-project.org/",
    "Maintainer": "Leo Lahti <leo.lahti@iki.fi>",
    "Author": "Leo Lahti, Olli-Pekka Huovilainen and Antonio Gusmao",
    "Title": "NetResponse: functional network analysis",
    "source.ver": "src/contrib/netresponse_1.0.2.tar.gz",
    "Package": "netresponse",
    "vignettes": [
      "vignettes/netresponse/inst/doc/netresponse.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL (>=2)",
    "biocViews": [
      "CellBiology",
      "Clustering",
      "DifferentialExpression",
      "GeneExpression",
      "Genetics",
      "Microarray",
      "Software",
      "Transcription"
    ],
    "Description": "Algorithms for functional network analysis. Also includes an implementation of a variational Dirichlet process Gaussian mixture model for nonparametric mixture modeling.",
    "win.binary.ver": "bin/windows/contrib/2.12/netresponse_1.0.2.zip"
  },
  "bioDist": {
    "Depends": [
      "R (>= 2.0)",
      "methods",
      "Biobase",
      "KernSmooth"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/bioDist_1.22.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/bioDist_1.22.0.tgz",
    "Version": "1.22.0",
    "dependsOnMe": [
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    ],
    "Maintainer": "Biocore Team c/o BioC user list <bioconductor@stat.math.ethz.ch>",
    "Author": "B. Ding, R. Gentleman and Vincent Carey",
    "Title": "Different distance measures",
    "suggestsMe": [
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    "source.ver": "src/contrib/bioDist_1.22.0.tar.gz",
    "Suggests": [
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    ],
    "Package": "bioDist",
    "vignettes": [
      "vignettes/bioDist/inst/doc/bioDist.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "Bioinformatics",
      "Software"
    ],
    "Description": "A collection of software tools for calculating distance measures.",
    "win.binary.ver": "bin/windows/contrib/2.12/bioDist_1.22.0.zip"
  },
  "simpleaffy": {
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      "R (>= 2.0.0)",
      "affy",
      "genefilter",
      "Biobase",
      "methods",
      "utils",
      "gcrma"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/simpleaffy_2.26.1.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/simpleaffy_2.26.1.tgz",
    "Version": "2.26.1",
    "dependsOnMe": [
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    "URL": "http://www.bioconductor.org, http://bioinformatics.picr.man.ac.uk/simpleaffy/",
    "Maintainer": "Crispin Miller <cmiller@picr.man.ac.uk>",
    "Author": "Crispin J Miller",
    "Title": "Very simple high level analysis of Affymetrix data",
    "suggestsMe": [
      "AffyExpress",
      "ArrayTools"
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    "source.ver": "src/contrib/simpleaffy_2.26.1.tar.gz",
    "Imports": [
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      "Biobase",
      "gcrma",
      "genefilter",
      "graphics",
      "grDevices",
      "methods",
      "stats",
      "utils"
    ],
    "Package": "simpleaffy",
    "vignettes": [
      "vignettes/simpleaffy/inst/doc/QCandSimpleaffy.pdf",
      "vignettes/simpleaffy/inst/doc/simpleAffy.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL (>= 2)",
    "biocViews": [
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      "Bioinformatics",
      "DataImport",
      "DifferentialExpression",
      "Microarray",
      "OneChannel",
      "Preprocessing",
      "QualityControl",
      "ReportWriting",
      "Software",
      "Transcription",
      "Visualization"
    ],
    "Description": "Provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. Makes heavy use of the affy library. Also has some basic scatter plot functions and mechanisms for generating high resolution journal figures...",
    "importsMe": [
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      "arrayMvout",
      "arrayQualityMetrics",
      "yaqcaffy"
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    "win.binary.ver": "bin/windows/contrib/2.12/simpleaffy_2.26.1.zip"
  },
  "tspair": {
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      "R (>= 2.2.1)",
      "Biobase (>= 2.4.0)",
      "time"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/tspair_1.8.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/tspair_1.8.0.tgz",
    "Version": "1.8.0",
    "Maintainer": "Jeffrey T. Leek <jtleek@jhu.edu>",
    "Author": "Jeffrey T. Leek <jtleek@jhu.edu>",
    "Title": "Top Scoring Pairs for Microarray Classification",
    "source.ver": "src/contrib/tspair_1.8.0.tar.gz",
    "Package": "tspair",
    "vignettes": [
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      "vignettes/tspair/inst/doc/tsp1.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL",
    "biocViews": [
      "Bioinformatics",
      "Microarray",
      "Software"
    ],
    "Description": "These functions calculate the pair of genes that show the maximum difference in ranking between two user specified groups. This \"top scoring pair\" maximizes the average of sensitivity and specificity over all rank based classifiers using a pair of genes in the data set. The advantage of classifying samples based on only the relative rank of a pair of genes is (a) the classifiers are much simpler and often more interpretable than more complicated classification schemes and (b) if arrays can be classified using only a pair of genes, PCR based tests could be used for classification of samples. See the references for the tspcalc() function for references regarding TSP classifiers.",
    "win.binary.ver": "bin/windows/contrib/2.12/tspair_1.8.0.zip"
  },
  "flowStats": {
    "Depends": [
      "R (>= 2.9.0)",
      "flowCore (>= 1.10.0)",
      "fda (>= 2.1.3)",
      "mvoutlier",
      "cluster"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/flowStats_1.8.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/flowStats_1.8.0.tgz",
    "Version": "1.8.0",
    "Maintainer": "Florian Hahne <fhahne@fhcrc.org> and Chao-Jen Wong <cwon2@fhcrc.org>",
    "Author": "Florian Hahne, Nishant Gopalakrishnan, Alireza Hadj Khodabakhshi, Chao-Jen Wong, Kyongryun Lee",
    "Title": "Statistical methods for the analysis of flow cytometry data",
    "source.ver": "src/contrib/flowStats_1.8.0.tar.gz",
    "Imports": [
      "MASS",
      "flowViz",
      "flowCore",
      "fda (>= 2.1.3)",
      "Biobase",
      "methods",
      "grDevices",
      "graphics",
      "stats",
      "utils",
      "KernSmooth",
      "lattice"
    ],
    "Suggests": [
      "flowViz",
      "xtable"
    ],
    "Package": "flowStats",
    "vignettes": [
      "vignettes/flowStats/inst/doc/GettingStartedWithFlowStats.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "Bioinformatics",
      "CellBasedAssays",
      "FlowCytometry",
      "Software"
    ],
    "Description": "Methods and functionality to analyse flow data that is beyond the basic infrastructure provided by the flowCore package.",
    "win.binary.ver": "bin/windows/contrib/2.12/flowStats_1.8.0.zip"
  },
  "ChemmineR": {
    "Depends": [
      "R (>= 2.10.0)",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/ChemmineR_2.2.19.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/ChemmineR_2.2.14.tgz",
    "Version": "2.2.19",
    "URL": "http://manuals.bioinformatics.ucr.edu/home/chemminer",
    "Maintainer": "ChemmineR Team <see@url>",
    "Author": "Y. Eddie Cao, Tyler Backman, Yan Wang, Thomas Girke",
    "Title": "Analysis of Small Molecule and Screening Data",
    "source.ver": "src/contrib/ChemmineR_2.2.19.tar.gz",
    "Imports": [
      "graphics",
      "methods",
      "stats",
      "RCurl"
    ],
    "Package": "ChemmineR",
    "vignettes": [
      "vignettes/ChemmineR/inst/doc/ChemmineR.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "Bioinformatics",
      "CellBasedAssays",
      "Clustering",
      "DataImport",
      "Infrastructure",
      "MicrotitrePlateAssay",
      "Proteomics",
      "Software",
      "Visualization"
    ],
    "Description": "ChemmineR is an R package for analyzing small molecule and screening data. The new version of the package 'ChemmineR-V2' contains efficient functions and data containers for processing SDFs (structure data files), structural similarity searching, clustering/diversity analyses of compound libraries with a wide spectrum of algorithms. In addition, it offers utilities for managing complex data sets from high-throughput compound bio-assays, and visualization functions for clustering results and chemical structures.",
    "win.binary.ver": "bin/windows/contrib/2.12/ChemmineR_2.2.19.zip"
  },
  "copa": {
    "Depends": [
      "Biobase",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/copa_1.18.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/copa_1.18.0.tgz",
    "Version": "1.18.0",
    "Maintainer": "James W. MacDonald <jmacdon@med.umich.edu>",
    "Author": "James W. MacDonald",
    "Title": "Functions to perform cancer outlier profile analysis.",
    "source.ver": "src/contrib/copa_1.18.0.tar.gz",
    "Suggests": [
      "colonCA"
    ],
    "Package": "copa",
    "vignettes": [
      "vignettes/copa/inst/doc/copa.pdf"
    ],
    "Archs": "i386, x64",
    "License": "Artistic-2.0",
    "biocViews": [
      "DifferentialExpression",
      "OneChannel",
      "Software",
      "TwoChannel",
      "Visualization"
    ],
    "Description": "COPA is a method to find genes that undergo recurrent fusion in a given cancer type by finding pairs of genes that have mutually exclusive outlier profiles.",
    "win.binary.ver": "bin/windows/contrib/2.12/copa_1.18.0.zip"
  },
  "idiogram": {
    "Depends": [
      "R (>= 2.0.0)",
      "methods",
      "Biobase",
      "annotate",
      "plotrix"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/idiogram_1.26.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/idiogram_1.26.0.tgz",
    "Version": "1.26.0",
    "dependsOnMe": [
      "reb"
    ],
    "Maintainer": "Karl J. Dykema <karl.dykema@vai.org>",
    "Author": "Karl J. Dykema <karl.dykema@vai.org>",
    "Title": "idiogram",
    "source.ver": "src/contrib/idiogram_1.26.0.tar.gz",
    "Suggests": [
      "hu6800.db",
      "golubEsets"
    ],
    "Package": "idiogram",
    "vignettes": [
      "vignettes/idiogram/inst/doc/idiogram.pdf"
    ],
    "License": "GPL-2",
    "biocViews": [
      "Software",
      "Visualization"
    ],
    "Description": "A package for plotting genomic data by chromosomal location",
    "win.binary.ver": "bin/windows/contrib/2.12/idiogram_1.26.0.zip"
  },
  "PICS": {
    "Depends": [
      "R(>= 2.11.0)",
      "IRanges",
      "GenomicRanges",
      "BSgenome"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/PICS_1.4.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/PICS_1.4.0.tgz",
    "Version": "1.4.0",
    "Maintainer": "Arnaud Droit <arnaud.droit@ircm.qc.ca>, Xuekui Zhang <xzhang@stat.ubc.ca>, Raphael Gottardo <raph@stat.ubc.ca>",
    "Author": "Xuekui Zhang <xzhang@stat.ubc.ca>, Raphael Gottardo <raph@stat.ubc.ca>",
    "Title": "Probabilistic inference of ChIP-seq",
    "source.ver": "src/contrib/PICS_1.4.0.tar.gz",
    "Imports": [
      "IRanges",
      "GenomicRanges",
      "BSgenome",
      "methods",
      "graphics",
      "grDevices",
      "stats"
    ],
    "Suggests": [
      "snowfall",
      "ShortRead",
      "rtracklayer"
    ],
    "Package": "PICS",
    "vignettes": [
      "vignettes/PICS/inst/doc/PICS.pdf"
    ],
    "Archs": "i386, x64",
    "License": "Artistic-2.0",
    "biocViews": [
      "ChIPseq",
      "Clustering",
      "Sequencing",
      "Software",
      "Statistics",
      "Visualization"
    ],
    "Description": "Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach.",
    "Enhances": [
      "multicore"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/PICS_1.4.0.zip"
  },
  "Category": {
    "Depends": [
      "AnnotationDbi (>= 0.1.15)",
      "Biobase (>= 1.15.29)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/Category_2.16.1.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/Category_2.16.1.tgz",
    "Version": "2.16.1",
    "dependsOnMe": [
      "eisa",
      "GOstats",
      "PCpheno"
    ],
    "Maintainer": "Biocore Team c/o BioC user list <bioconductor@stat.math.ethz.ch>",
    "Author": "R. Gentleman with contributions from S. Falcon and D.Sarkar",
    "Title": "Category Analysis",
    "suggestsMe": [
      "BiocCaseStudies",
      "cellHTS",
      "GSEAlm",
      "qpgraph"
    ],
    "source.ver": "src/contrib/Category_2.16.1.tar.gz",
    "Imports": [
      "graph",
      "methods",
      "Biobase (>= 1.15.29)",
      "AnnotationDbi (>= 0.1.15)",
      "RBGL",
      "GSEABase",
      "genefilter",
      "annotate (>= 1.15.6)",
      "stats",
      "utils"
    ],
    "Suggests": [
      "EBarrays",
      "ALL",
      "Rgraphviz",
      "RColorBrewer",
      "xtable (>= 1.4-6)",
      "hgu95av2.db",
      "Matrix",
      "KEGG.db",
      "GO.db",
      "SNPchip",
      "geneplotter",
      "limma",
      "lattice",
      "graph",
      "Biobase",
      "genefilter",
      "methods"
    ],
    "Package": "Category",
    "vignettes": [
      "vignettes/Category/inst/doc/Category.pdf",
      "vignettes/Category/inst/doc/ChromBand.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "Annotation",
      "Bioinformatics",
      "GO",
      "Pathways",
      "Software"
    ],
    "Description": "A collection of tools for performing category analysis.",
    "importsMe": [
      "cellHTS2",
      "GOstats",
      "PCpheno",
      "ppiStats"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/Category_2.16.1.zip"
  },
  "CNVtools": {
    "Depends": [
      "survival"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/CNVtools_1.44.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/CNVtools_1.44.0.tgz",
    "Version": "1.44.0",
    "Maintainer": "Chris Barnes <christopher.barnes@imperial.ac.uk>",
    "Author": "Chris Barnes <christopher.barnes@imperial.ac.uk> and Vincent Plagnol <vincent.plagnol@cimr.cam.ac.uk>",
    "Title": "A package to test genetic association with CNV data",
    "source.ver": "src/contrib/CNVtools_1.44.0.tar.gz",
    "Package": "CNVtools",
    "vignettes": [
      "vignettes/CNVtools/inst/doc/CNVtools-vignette.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL-3",
    "biocViews": [
      "DNACopyNumber",
      "GeneticVariability",
      "Software"
    ],
    "Description": "This package is meant to facilitate the testing of Copy Number Variant data for genetic association, typically in case-control studies.",
    "win.binary.ver": "bin/windows/contrib/2.12/CNVtools_1.44.0.zip"
  },
  "NuPoP": {
    "win64.binary.ver": "bin/windows64/contrib/2.12/NuPoP_1.0.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/NuPoP_1.0.0.tgz",
    "Version": "1.0.0",
    "Maintainer": "Ji-Ping Wang<jzwang@northwestern.edu>",
    "Author": "Ji-Ping Wang <jzwang@northwestern.edu>; Liqun Xi <lxi700@northwestern.edu>",
    "Title": "An R package for nucleosome positioning prediction",
    "source.ver": "src/contrib/NuPoP_1.0.0.tar.gz",
    "Package": "NuPoP",
    "vignettes": [
      "vignettes/NuPoP/inst/doc/NuPoP-intro.pdf",
      "vignettes/NuPoP/inst/doc/NuPoP-manual.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL-2",
    "biocViews": [
      "Software",
      "classification",
      "genetics",
      "visualization"
    ],
    "Description": "NuPoP is an R package for Nucleosome Positioning Prediction.This package is built upon a duration hidden Markov model proposed in Xi et al, 2010; Wang et al, 2008. The core of the package was written in Fotran. In addition to the R package, a stand-alone Fortran software tool is also available at http://nucleosome.stats.northwestern.edu.",
    "win.binary.ver": "bin/windows/contrib/2.12/NuPoP_1.0.0.zip"
  },
  "DNAcopy": {
    "win64.binary.ver": "bin/windows64/contrib/2.12/DNAcopy_1.24.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/DNAcopy_1.24.0.tgz",
    "Version": "1.24.0",
    "dependsOnMe": [
      "CGHcall",
      "cghMCR",
      "snapCGH"
    ],
    "Maintainer": "Venkatraman E. Seshan <seshanv@mskcc.org>",
    "Author": "Venkatraman E. Seshan, Adam Olshen",
    "Title": "DNA copy number data analysis",
    "suggestsMe": [
      "ADaCGH2",
      "beadarraySNP"
    ],
    "source.ver": "src/contrib/DNAcopy_1.24.0.tar.gz",
    "Package": "DNAcopy",
    "vignettes": [
      "vignettes/DNAcopy/inst/doc/DNAcopy.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL (>= 2)",
    "biocViews": [
      "CopyNumberVariants",
      "Microarray",
      "Software"
    ],
    "Description": "Segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number",
    "importsMe": [
      "snapCGH"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/DNAcopy_1.24.0.zip"
  },
  "occugene": {
    "Depends": [
      "R (>= 2.0.0)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/occugene_1.10.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/occugene_1.10.0.tgz",
    "Version": "1.10.0",
    "Maintainer": "Oliver Will <oliverrreader@gmail.com>",
    "Author": "Oliver Will <oliverrreader@gmail.com>",
    "Title": "Functions for Multinomial Occupancy Distribution",
    "source.ver": "src/contrib/occugene_1.10.0.tar.gz",
    "Package": "occugene",
    "vignettes": [
      "vignettes/occugene/inst/doc/occugene.pdf"
    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "Annotation",
      "Bioinformatics",
      "Pathways",
      "Software"
    ],
    "Description": "Statistical tools for building random mutagenesis libraries for prokaryotes. The package has functions for handling the occupancy distribution for a multinomial and for estimating the number of essential genes in random transposon mutagenesis libraries.",
    "win.binary.ver": "bin/windows/contrib/2.12/occugene_1.10.0.zip"
  },
  "BUS": {
    "Depends": [
      "R (>= 2.3.0)",
      "minet"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/BUS_1.6.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/BUS_1.6.0.tgz",
    "Version": "1.6.0",
    "Maintainer": "Yuanhua Liu <liuyuanhua@picb.ac.cn>",
    "Author": "Yin Jin, Hesen Peng, Lei Wang, Raffaele Fronza, Yuanhua Liu and Christine Nardini",
    "Title": "Gene network reconstruction",
    "source.ver": "src/contrib/BUS_1.6.0.tar.gz",
    "Imports": [
      "stats"
    ],
    "Package": "BUS",
    "vignettes": [
      "vignettes/BUS/inst/doc/bus.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL-3",
    "biocViews": [
      "Preprocessing",
      "Software",
      "Statistics"
    ],
    "Description": "This package can be used to compute associations among genes (gene-networks) or between genes and some external traits (i.e. clinical).",
    "win.binary.ver": "bin/windows/contrib/2.12/BUS_1.6.0.zip"
  },
  "GeneAnswers": {
    "Depends": [
      "R (>= 2.10.0)",
      "igraph",
      "RCurl",
      "annotate",
      "Biobase (>= 1.12.0)",
      "methods",
      "XML",
      "RSQLite",
      "MASS",
      "rgl",
      "Heatplus",
      "RColorBrewer"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/GeneAnswers_1.6.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/GeneAnswers_1.6.0.tgz",
    "Version": "1.6.0",
    "Maintainer": "Gang Feng <g-feng@northwestern.edu> and Pan Du <dupan@northwestern.edu>",
    "Author": "Gang Feng, Pan Du, Tian Xia, Warren Kibbe and Simon Lin",
    "Title": "Integrated Interpretation of Genes",
    "source.ver": "src/contrib/GeneAnswers_1.6.0.tar.gz",
    "Imports": [
      "graph",
      "Rgraphviz",
      "RBGL",
      "annotate"
    ],
    "Suggests": [
      "GO.db",
      "KEGG.db",
      "biomaRt",
      "AnnotationDbi",
      "org.Hs.eg.db",
      "org.Rn.eg.db",
      "org.Mm.eg.db",
      "org.Dm.eg.db"
    ],
    "Package": "GeneAnswers",
    "vignettes": [
      "vignettes/GeneAnswers/inst/doc/geneAnswers.pdf",
      "vignettes/GeneAnswers/inst/doc/geneFunctionSummarize.pdf"
    ],
    "License": "LGPL (>= 2)",
    "biocViews": [
      "DataRepresentation",
      "GraphsAndNetworks",
      "Infrastructure",
      "Software",
      "Visualization"
    ],
    "Description": "GeneAnswers provide an integrated tool for biological or medical interpretation of the given one or more groups of genes by means of statistical test.",
    "win.binary.ver": "bin/windows/contrib/2.12/GeneAnswers_1.6.0.zip"
  },
  "HilbertVisGUI": {
    "Depends": [
      "R (>= 2.6.0)",
      "HilbertVis (>= 1.1.6)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/HilbertVisGUI_1.8.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/HilbertVisGUI_1.8.0.tgz",
    "Version": "1.8.0",
    "URL": "http://www.ebi.ac.uk/~anders/hilbert",
    "Maintainer": "Simon Anders <anders@fs.tum.de>",
    "Author": "Simon Anders <anders@fs.tum.de>",
    "Title": "HilbertVisGUI",
    "source.ver": "src/contrib/HilbertVisGUI_1.8.0.tar.gz",
    "Suggests": [
      "lattice",
      "IRanges"
    ],
    "Package": "HilbertVisGUI",
    "vignettes": [
      "vignettes/HilbertVisGUI/inst/doc/HilbertVisGUI.pdf"
    ],
    "Archs": "i386",
    "License": "GPL (>= 3)",
    "biocViews": [
      "Software",
      "Visualization"
    ],
    "Description": "An interactive tool to visualize long vectors of integer data by means of Hilbert curves",
    "SystemRequirements": "gtkmm-2.4",
    "win.binary.ver": "bin/windows/contrib/2.12/HilbertVisGUI_1.8.0.zip"
  },
  "BayesPeak": {
    "Depends": [
      "IRanges"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/BayesPeak_1.2.3.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/BayesPeak_1.2.3.tgz",
    "Version": "1.2.3",
    "Maintainer": "Jonathan Cairns <jmc200@cam.ac.uk>",
    "Author": "Christiana Spyrou, Jonathan Cairns, Rory Stark, Andy Lynch, Simon Tavar\\\\'{e},",
    "Title": "Bayesian Analysis of ChIP-seq Data",
    "source.ver": "src/contrib/BayesPeak_1.2.3.tar.gz",
    "Imports": [
      "IRanges",
      "graphics"
    ],
    "Package": "BayesPeak",
    "vignettes": [
      "vignettes/BayesPeak/inst/doc/BayesPeak.pdf",
      "vignettes/BayesPeak/inst/doc/regionOFdiag.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL (>= 2)",
    "biocViews": [
      "ChIPseq",
      "Software"
    ],
    "Description": "This package is an implementation of the BayesPeak algorithm for peak calling in ChIP-seq data.",
    "Enhances": [
      "multicore"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/BayesPeak_1.2.3.zip"
  },
  "plateCore": {
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      "R (>= 2.8.0)",
      "flowCore",
      "flowViz",
      "lattice",
      "latticeExtra"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/plateCore_1.8.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/plateCore_1.8.0.tgz",
    "Version": "1.8.0",
    "URL": "http://www.bioconductor.org",
    "Maintainer": "Errol Strain <estrain@gmail.com>",
    "Author": "Errol Strain, Florian Hahne, and Perry Haaland",
    "Title": "Statistical tools and data structures for plate-based flow cytometry",
    "source.ver": "src/contrib/plateCore_1.8.0.tar.gz",
    "Imports": [
      "Biobase",
      "flowCore",
      "graphics",
      "grDevices",
      "lattice",
      "MASS",
      "methods",
      "robustbase",
      "stats",
      "utils"
    ],
    "Suggests": [
      "gplots"
    ],
    "Package": "plateCore",
    "vignettes": [
      "vignettes/plateCore/inst/doc/expDens.pdf",
      "vignettes/plateCore/inst/doc/plateCoreVig.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "CellBasedAssays",
      "Flowcytometry",
      "Infrastructure",
      "Software"
    ],
    "Description": "Provides basic S4 data structures and routines for analyzing plate based flow cytometry data.",
    "win.binary.ver": "bin/windows/contrib/2.12/plateCore_1.8.0.zip"
  },
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    "Depends": [
      "R (>= 2.6.0)",
      "Biobase (>= 1.15.33)",
      "limma (>= 1.7.0)",
      "marray",
      "utils",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/convert_1.26.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/convert_1.26.0.tgz",
    "Version": "1.26.0",
    "dependsOnMe": [
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    ],
    "URL": "http://bioinf.wehi.edu.au/limma/convert.html",
    "Maintainer": "Yee Hwa (Jean) Yang <jean@biostat.ucsf.edu>",
    "Author": "Gordon Smyth <smyth@wehi.edu.au>, James Wettenhall <wettenhall@wehi.edu.au>, Yee Hwa (Jean Yang) <jean@biostat.ucsf.edu>, Martin Morgan <mtmorgan@fhcrc.org>Martin Morgan",
    "Title": "Convert Microarray Data Objects",
    "suggestsMe": [
      "BiocCaseStudies",
      "dyebias",
      "dyebiasexamples",
      "OLIN"
    ],
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    "Maintainer": "Yuanhua Liu <liuyuanhua@picb.ac.cn>",
    "Author": "Wei Xiao, Yin Jin, Darong Lai, Xinyi Yang, Yuanhua Liu, Christine Nardini",
    "Title": "Predict gene network using an Ordinary Differential Equation (ODE) based method",
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    "Author": "Vince Carey <stvjc@channing.harvard.edu>, Li Long <li.long@isb-sib.ch>, R. Gentleman",
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    "Description": "Functions to computationally simulate the AP-MS technology based on wet-lab data.",
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    "Author": "Francesco Favero",
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    "Description": "Useful functions to merge microRNA and respective targets using differents databases",
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      "snapCGH"
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    "URL": "http://bioinf.wehi.edu.au/limma",
    "Maintainer": "Gordon Smyth <smyth@wehi.edu.au>",
    "Author": "Gordon Smyth with contributions from Matthew Ritchie, Jeremy Silver, James Wettenhall, Natalie Thorne, Mette Langaas, Egil Ferkingstad, Marcus Davy, Francois Pepin, Dongseok Choi, Davis McCarthy, Di Wu, Alicia Oshlack, Carolyn de Graaf, Yifang Hu, Wei Shi and Belinda Phipson.",
    "Title": "Linear Models for Microarray Data",
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      "CMA",
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    "Maintainer": "Tony Chiang <tchiang@fhcrc.org>",
    "Author": "Tony Chiang <tchiang@fhcrc.org>",
    "Title": "In Silico Interactome",
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    "Description": "Package to create In Silico Interactomes",
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    "Maintainer": "Hui Zhao <hui.zhao@biw.kuleuven.be>",
    "Author": "Hui Zhao, Kristof Engelen, Bart De Moor and Kathleen Marchal",
    "Title": "Calibration model for estimating absolute expression levels from microarray data",
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    "Archs": "i386, x64",
    "License": "LGPL",
    "biocViews": [
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      "TwoChannel"
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    "Description": "This package contains functions for normalizing spotted microarray data, based on a physically motivated calibration model. The model parameters and error distributions are estimated from external control spikes.",
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    "URL": "http://www.genopolis.it",
    "Maintainer": "Norman Pavelka <normanpavelka@gmail.com>",
    "Author": "Mattia Pelizzola <mattia.pelizzola@gmail.com> and Norman Pavelka <normanpavelka@gmail.com>",
    "Title": "Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)",
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    "Imports": [
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    "License": "GPL",
    "biocViews": [
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      "Microarray",
      "Proteomics",
      "Software"
    ],
    "Description": "The Power Law Global Error Model (PLGEM) has been shown to faithfully model the variance-versus-mean dependence that exists in a variety of genome-wide datasets, including microarray and proteomics data. The use of PLGEM has been shown to improve the detection of differentially expressed genes or proteins in these datasets.",
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    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/RankProd_2.22.0.zip",
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    "Maintainer": "Fangxin Hong <fxhong@jimmy.harvard.edu>",
    "Author": "Fangxin Hong <fxhong@jimmy.harvard.edu> and Ben Wittner <Wittner.Ben@mgh.harvard.edu> with contribution from Rainer Breitling <r.breitling@bio.gla.ac.uk> and Colin Smith <colin@colinsmith.org>",
    "Title": "Rank Product method for identifying differentially expressed genes with application in meta-analysis",
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    "vignettes": [
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    "License": "file LICENSE",
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    "Description": "Non-paramteric method for identifying differentially expressed (up- or down- regulated )genes based on the estimated percentage of false predictions (pfp).The method can combine data sets from different origins (meta-analysis)to increase the power of the identification.",
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    "Author": "Li Long <lilong@isb-sib.ch>",
    "Title": "Render molecular pathways",
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    "Maintainer": "Aedin Culhane <Aedin@jimmy.harvard.edu>",
    "Author": "Aedin Culhane",
    "Title": "Multivariate analysis of microarray data using ADE4",
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    "Suggests": [
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      "vignettes/made4/inst/doc/introduction.pdf"
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    "License": "Artistic-2.0",
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    "Description": "Multivariate data analysis and graphical display of microarray data. Functions include between group analysis and coinertia analysis. It contains functions that require ADE4.",
    "win.binary.ver": "bin/windows/contrib/2.12/made4_1.24.0.zip"
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      "R (>= 2.11.0)",
      "affy",
      "affydata",
      "methods"
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    "Maintainer": "Leo Lahti <leo.lahti@iki.fi>",
    "Author": "Leo Lahti <leo.lahti@iki.fi>",
    "Title": "RPA: probe reliability and differential gene expression analysis",
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    "License": "GPL (>= 2)",
    "biocViews": [
      "GeneExpression",
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      "Preprocessing",
      "QualityControl",
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    "Description": "Probabilistic analysis of probe reliability and differential gene expression on short oligonucleotide arrays as described in Leo Lahti et al. \"Probabilistic Analysis of Probe Reliability in Differential Gene Expression Studies with Short Oligonucleotide Arrays\", TCBB/IEEE, to appear. See http://doi.ieeecomputersociety.org/10.1109/TCBB.2009.38",
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    "Version": "1.14.0",
    "URL": "http://www.bmbolstad.com",
    "Maintainer": "B. M. Bolstad <bmb@bmbolstad.com>",
    "Author": "B. M. Bolstad <bmb@bmbolstad.com>",
    "Title": "Microarray Data related methods that utlize BufferedMatrix objects",
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    "Suggests": [
      "affyio",
      "affy"
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    "Package": "BufferedMatrixMethods",
    "Archs": "i386, x64",
    "License": "GPL (>= 2)",
    "LinkingTo": "BufferedMatrix",
    "biocViews": [
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      "Software"
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    "Description": "Microarray analysis methods that use BufferedMatrix objects",
    "win.binary.ver": "bin/windows/contrib/2.12/BufferedMatrixMethods_1.14.0.zip"
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      "methods"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/SMAP_1.14.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/SMAP_1.14.0.tgz",
    "Version": "1.14.0",
    "Maintainer": "Robin Andersson <robin.andersson@lcb.uu.se>",
    "Author": "Robin Andersson <robin.andersson@lcb.uu.se>",
    "Title": "A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling",
    "source.ver": "src/contrib/SMAP_1.14.0.tar.gz",
    "Package": "SMAP",
    "vignettes": [
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    ],
    "Archs": "i386, x64",
    "License": "GPL-2",
    "biocViews": [
      "CopyNumberVariants",
      "Microarray",
      "Software",
      "TwoChannel"
    ],
    "Description": "Functions and classes for DNA copy number profiling of array-CGH data",
    "win.binary.ver": "bin/windows/contrib/2.12/SMAP_1.14.0.zip"
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      "R(>= 2.4.0)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/SLqPCR_1.16.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/SLqPCR_1.16.0.tgz",
    "Version": "1.16.0",
    "Maintainer": "Matthias Kohl <kohl@sirs-lab.com>",
    "Author": "Matthias Kohl",
    "Title": "Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH",
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    "Imports": [
      "stats"
    ],
    "Suggests": [
      "RColorBrewer"
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    "Package": "SLqPCR",
    "vignettes": [
      "vignettes/SLqPCR/inst/doc/SLqPCR.pdf"
    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "Bioinformatics",
      "Software"
    ],
    "Description": "Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH",
    "win.binary.ver": "bin/windows/contrib/2.12/SLqPCR_1.16.0.zip"
  },
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    "Depends": [
      "Rgraphviz",
      "graph"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/biocGraph_1.12.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/biocGraph_1.12.0.tgz",
    "Version": "1.12.0",
    "Maintainer": "Florian Hahne <fhahne@fhcrc.org>",
    "Author": "Li Long <li.long@isb-sib.ch>, Robert Gentleman <rgentlem@fhcrc.org>, Seth Falcon <sethf@fhcrc.org> Florian Hahne <fhahne@fhcrc.org>",
    "Title": "Graph examples and use cases in Bioinformatics",
    "suggestsMe": [
      "BiocCaseStudies",
      "RTools4TB"
    ],
    "source.ver": "src/contrib/biocGraph_1.12.0.tar.gz",
    "Imports": [
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      "geneplotter",
      "graph",
      "methods"
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      "fibroEset",
      "geneplotter",
      "hgu95av2.db"
    ],
    "Package": "biocGraph",
    "vignettes": [
      "vignettes/biocGraph/inst/doc/biocGraph.pdf",
      "vignettes/biocGraph/inst/doc/layingOutPathways.pdf"
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    "License": "Artistic-2.0",
    "biocViews": [
      "GraphsAndNetworks",
      "Software"
    ],
    "Description": "This package provides examples and code that make use of the different graph related packages produced by Bioconductor.",
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    "Depends": [
      "tcltk",
      "tkrplot",
      "IsoGene"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/IsoGeneGUI_1.2.1.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/IsoGeneGUI_1.2.1.tgz",
    "Version": "1.2.1",
    "URL": "http://www.ibiostat.be/software/IsoGeneGUI/index.html",
    "Maintainer": "Setia Pramana <setia.pramana@uhasselt.be>",
    "Author": "Setia Pramana, Dan Lin, Philippe Haldermans, Tobias Verbeke",
    "Title": "A graphical user interface to conduct a dose-response analysis of microarray data",
    "source.ver": "src/contrib/IsoGeneGUI_1.2.1.tar.gz",
    "Imports": [
      "multtest",
      "relimp",
      "WriteXLS",
      "gdata",
      "RColorBrewer",
      "geneplotter"
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    "Suggests": [
      "RUnit"
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    "Package": "IsoGeneGUI",
    "vignettes": [
      "vignettes/IsoGeneGUI/inst/doc/IsoGeneGUI.pdf"
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    "License": "GPL-2",
    "biocViews": [
      "DifferentialExpression",
      "GUI",
      "Microarray",
      "Software",
      "Statistics"
    ],
    "Description": "The IsoGene Graphical User Interface (IsoGene-GUI) is a user friendly interface of the IsoGene package which is aimed to identify for genes with a monotonic trend in the expression levels with respect to the increasing doses using several test statistics: global likelihood ratio test (E2), Bartholomew 1961, Barlow et al. 1972 and Robertson et al. 1988), Williams (1971, 1972), Marcus (1976), the M (Hu et al. 2005) and the modified M (Lin et al. 2007).  The p-values of the global likelihood ratio test (E2) are obtained using the excat distribution and permutation. The other four test statistics are obtained using permutation . Several p-values adjustment are provided: Bonferroni, Holm (1979), Hochberg (1988), and Sidak procedures for controlling the family-wise Type I error rate (FWER), and BH (Benjamini and Hochberg 1995) and BY (Benjamini and Yekutieli 2001) procedures are used for controlling the FDR. the inference is based on resampling methods, which control the False Discovery Rate (FDR) (both permutations (Ge et al., 2003) and the Significance Analysis of Microarrays (SAM), Tusher et al., 2001).",
    "win.binary.ver": "bin/windows/contrib/2.12/IsoGeneGUI_1.2.1.zip"
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      "R(>= 2.9.0)",
      "IRanges",
      "Biobase",
      "affxparser"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/rMAT_3.0.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/rMAT_3.0.0.tgz",
    "Version": "3.0.0",
    "URL": "http://www.rglab.org",
    "Maintainer": "Arnaud Droit <arnaud.droit@ircm.qc.ca> and Raphael Gottardo <raphael.gottardo@ircm.qc.ca>",
    "Author": "Charles Cheung and Arnaud Droit and Raphael Gottardo",
    "Title": "R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data.",
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    "Imports": [
      "Biobase (>= 2.5.5)",
      "methods",
      "IRanges"
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      "rtracklayer"
    ],
    "Package": "rMAT",
    "vignettes": [
      "vignettes/rMAT/inst/doc/rMAT.pdf"
    ],
    "Archs": "i386, x64",
    "License": "Artistic-2.0",
    "biocViews": [
      "Microarray",
      "Preprocessing",
      "Software",
      "Statistics"
    ],
    "Description": "This package is an R version of the package MAT and contains functions to parse and merge Affymetrix BPMAP and CEL tiling array files (using C++ based Fusion SDK and Bioconductor package affxparser), normalize tiling arrays using sequence specific models, detect enriched regions from ChIP-chip experiments. Note: users should have GSL anf GenomeGraphs installed. Windows users: 'consult the README file available in the inst directory of the source distribution for necessary configuration instructions'. Snow Leopard users can take advantage of increase speed with Grand Central Dispatch!",
    "win.binary.ver": "bin/windows/contrib/2.12/rMAT_3.0.0.zip"
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      "R (>= 2.10.0)",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/affyILM_1.2.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/affyILM_1.2.0.tgz",
    "Version": "1.2.0",
    "Maintainer": "Myriam Kroll and Fabrice Berger <affyILM@itf.fys.kuleuven.be>",
    "Author": "K. Myriam Kroll, Fabrice Berger, Gerard Barkema, Enrico Carlon",
    "Title": "Linear Model of background subtraction and the Langmuir isotherm",
    "source.ver": "src/contrib/affyILM_1.2.0.tar.gz",
    "Imports": [
      "affxparser (>= 1.16.0)",
      "gcrma",
      "affy",
      "graphics",
      "methods"
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    "Suggests": [
      "AffymetrixDataTestFiles"
    ],
    "Package": "affyILM",
    "vignettes": [
      "vignettes/affyILM/inst/doc/affyILM.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL-3",
    "biocViews": [
      "Microarray",
      "OneChannel",
      "Preprocessing",
      "Software"
    ],
    "Description": "affyILM is a preprocessing tool which estimates gene expression levels for Affymetrix Gene Chips. Input from physical chemistry is employed to first background subtract intensities before calculating concentrations on behalf of the Langmuir model.",
    "SystemRequirements": "Gnu Scientific Library version >= 1.8",
    "win.binary.ver": "bin/windows/contrib/2.12/affyILM_1.2.0.zip"
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  "Rdbi": {
    "Depends": [
      "R (>= 1.2)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/Rdbi_1.24.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/Rdbi_1.24.0.tgz",
    "Version": "1.24.0",
    "dependsOnMe": [
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    ],
    "Maintainer": "Jianhua Zhang <jzhang@jimmy.harvard.edu>",
    "Author": "Timothy H. Keitt <thk@users.sourceforge.net>",
    "Title": "Generic database methods",
    "source.ver": "src/contrib/Rdbi_1.24.0.tar.gz",
    "Package": "Rdbi",
    "License": "GPL",
    "biocViews": [
      "Infrastructure",
      "Software"
    ],
    "Description": "Generic framework for database access in R. Code written by Timothy H. Keitt and modified by Jianhua Zhang",
    "importsMe": [
      "pgUtils"
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    "win.binary.ver": "bin/windows/contrib/2.12/Rdbi_1.24.0.zip"
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      "methods"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/xps_1.10.2.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/xps_1.10.2.tgz",
    "Version": "1.10.2",
    "Maintainer": "Christian Stratowa <cstrato@aon.at>",
    "Author": "Christian Stratowa, Vienna, Austria",
    "Title": "Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays",
    "source.ver": "src/contrib/xps_1.10.2.tar.gz",
    "Package": "xps",
    "vignettes": [
      "vignettes/xps/inst/doc/APTvsXPS.pdf",
      "vignettes/xps/inst/doc/xps.pdf",
      "vignettes/xps/inst/doc/xpsClasses.pdf",
      "vignettes/xps/inst/doc/xpsPreprocess.pdf"
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    "Archs": "i386",
    "License": "GPL (>= 2.0)",
    "biocViews": [
      "DataImport",
      "DifferentialExpression",
      "ExonArray",
      "GeneExpression",
      "Microarray",
      "OneChannel",
      "Preprocessing",
      "Software",
      "Transcription"
    ],
    "Description": "The package handles pre-processing, normalization, filtering and analysis of Affymetrix GeneChip expression arrays, including exon arrays (Exon 1.0 ST: core, extended, full probesets), gene arrays (Gene 1.0 ST) and plate arrays on computers with 1 GB RAM only. It imports Affymetrix .CDF, .CLF, .PGF and .CEL as well as annotation files, and computes e.g. RMA, MAS5, FARMS, DFW, MAS5-calls, DABG-calls, I/NI-calls, FIRMA. It is an R wrapper to XPS (eXpression Profiling System), which is based on ROOT, an object-oriented framework developed at CERN. Thus, the prior installation of ROOT is a prerequisite for the usage of this package, however, no knowledge of ROOT is required. ROOT is licensed under LGPL and can be downloaded from http://root.cern.ch.",
    "SystemRequirements": "root_v5.27.04 <http://root.cern.ch> - See README file for installation instructions.",
    "win.binary.ver": "bin/windows/contrib/2.12/xps_1.10.2.zip"
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      "methods"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/xcms_1.24.1.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/xcms_1.24.1.tgz",
    "Version": "1.24.1",
    "dependsOnMe": [
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      "TargetSearch"
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    "URL": "http://metlin.scripps.edu/download/",
    "Maintainer": "Colin A. Smith <csmith@scripps.edu>",
    "Author": "Colin A. Smith <csmith@scripps.edu>, Ralf Tautenhahn <rtautenh@scripps.edu>, Steffen Neumann <sneumann@ipb-halle.de>, Paul Benton <hpaul.benton08@imperial.ac.uk>",
    "Title": "LC/MS and GC/MS Data Analysis",
    "suggestsMe": [
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      "MassSpecWavelet",
      "msdata"
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    "source.ver": "src/contrib/xcms_1.24.1.tar.gz",
    "Suggests": [
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      "multtest",
      "ncdf",
      "rgl",
      "MassSpecWavelet (>= 1.5.2)",
      "RANN",
      "snow",
      "KEGGSOAP"
    ],
    "Package": "xcms",
    "vignettes": [
      "vignettes/xcms/inst/doc/FlowChart.pdf",
      "vignettes/xcms/inst/doc/xcmsDirect.pdf",
      "vignettes/xcms/inst/doc/xcmsInstall.pdf",
      "vignettes/xcms/inst/doc/xcmsMSn.pdf",
      "vignettes/xcms/inst/doc/xcmsPreprocess.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL (>= 2)",
    "biocViews": [
      "MassSpectrometry",
      "Software",
      "Technology"
    ],
    "Description": "Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.",
    "SystemRequirements": "NetCDF, zlib",
    "Enhances": [
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      "XML"
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    "importsMe": [
      "CAMERA",
      "flagme"
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  },
  "topGO": {
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      "methods",
      "graph (>= 1.14.0)",
      "Biobase (>= 2.0.0)",
      "GO.db (>= 2.3.0)",
      "AnnotationDbi (>= 1.7.19)",
      "SparseM (>= 0.73)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/topGO_2.2.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/topGO_2.2.0.tgz",
    "Version": "2.2.0",
    "dependsOnMe": [
      "RNAither"
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    "Maintainer": "Adrian Alexa <alexa@mpi-inf.mpg.de>",
    "Author": "Adrian Alexa, Jorg Rahnenfuhrer",
    "Title": "topGO: Enrichment analysis for Gene Ontology",
    "suggestsMe": [
      "Ringo"
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    "source.ver": "src/contrib/topGO_2.2.0.tar.gz",
    "Imports": [
      "methods",
      "graph",
      "Biobase",
      "SparseM",
      "AnnotationDbi",
      "lattice"
    ],
    "Suggests": [
      "ALL",
      "hgu95av2.db",
      "hgu133a.db",
      "genefilter",
      "xtable",
      "multtest",
      "Rgraphviz",
      "globaltest"
    ],
    "Package": "topGO",
    "vignettes": [
      "vignettes/topGO/inst/doc/topGO_classes_v3.pdf",
      "vignettes/topGO/inst/doc/topGO.pdf"
    ],
    "License": "LGPL",
    "biocViews": [
      "Bioinformatics",
      "Microarray",
      "Software",
      "Visualization"
    ],
    "Description": "topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.",
    "win.binary.ver": "bin/windows/contrib/2.12/topGO_2.2.0.zip"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/MeasurementError.cor_1.22.0.tgz",
    "Version": "1.22.0",
    "Maintainer": "Beiying Ding <bding@amgen.com>",
    "Author": "Beiying Ding",
    "Title": "Measurement Error model estimate for correlation coefficient",
    "source.ver": "src/contrib/MeasurementError.cor_1.22.0.tar.gz",
    "Package": "MeasurementError.cor",
    "vignettes": [
      "vignettes/MeasurementError.cor/inst/doc/MeasurementError.cor.pdf"
    ],
    "License": "LGPL",
    "biocViews": [
      "Bioinformatics",
      "Software"
    ],
    "Description": "Two-stage measurement error model for correlation estimation with smaller bias than the usual sample correlation",
    "win.binary.ver": "bin/windows/contrib/2.12/MeasurementError.cor_1.22.0.zip"
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      "cellHTS2",
      "limma",
      "locfit"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/coRNAi_1.0.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/coRNAi_1.0.0.tgz",
    "Version": "1.0.0",
    "Maintainer": "Elin Axelsson <elin@ebi.ac.uk>",
    "Author": "Elin Axelsson",
    "Title": "Analysis of co-knock-down RNAi data",
    "source.ver": "src/contrib/coRNAi_1.0.0.tar.gz",
    "Imports": [
      "MASS",
      "gplots",
      "lattice",
      "grDevices",
      "graphics",
      "stats"
    ],
    "Package": "coRNAi",
    "vignettes": [
      "vignettes/coRNAi/inst/doc/coRNAi.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "CellBasedAssays",
      "Software"
    ],
    "Description": "Analysis of combinatorial cell-based RNAi screens",
    "SystemRequirements": "Graphviz",
    "win.binary.ver": "bin/windows/contrib/2.12/coRNAi_1.0.0.zip"
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      "R (>= 2.5.0)",
      "methods",
      "Biobase",
      "GO.db",
      "KEGG.db"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/annaffy_1.22.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/annaffy_1.22.0.tgz",
    "Version": "1.22.0",
    "dependsOnMe": [
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    ],
    "Maintainer": "Colin A. Smith <annaffy@colinsmith.org>",
    "Author": "Colin A. Smith <annaffy@colinsmith.org>",
    "Title": "Annotation tools for Affymetrix biological metadata",
    "suggestsMe": [
      "AffyExpress",
      "ArrayTools",
      "BiocCaseStudies",
      "maDB",
      "oneChannelGUI"
    ],
    "source.ver": "src/contrib/annaffy_1.22.0.tar.gz",
    "Imports": [
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    ],
    "Suggests": [
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      "multtest",
      "tcltk"
    ],
    "Package": "annaffy",
    "vignettes": [
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    ],
    "License": "LGPL",
    "biocViews": [
      "Annotation",
      "GO",
      "Microarray",
      "OneChannel",
      "Pathways",
      "ReportWriting",
      "Software"
    ],
    "Description": "Functions for handling data from Bioconductor Affymetrix annotation data packages. Produces compact HTML and text reports including experimental data and URL links to many online databases. Allows searching biological metadata using various criteria.",
    "importsMe": [
      "affycoretools",
      "GGtools"
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    "win.binary.ver": "bin/windows/contrib/2.12/annaffy_1.22.0.zip"
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      "R (>= 2.9.0)",
      "annotate (>= 1.20.0)",
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/ChromHeatMap_1.4.0.tgz",
    "Version": "1.4.0",
    "Maintainer": "Tim F. Rayner <tfrayner@gmail.com>",
    "Author": "Tim F. Rayner",
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    "Imports": [
      "annotate",
      "AnnotationDbi",
      "Biobase",
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      "methods",
      "stats",
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      "rtracklayer"
    ],
    "Suggests": [
      "ALL"
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    "Package": "ChromHeatMap",
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    ],
    "License": "Artistic-2.0",
    "biocViews": [
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      "Visualization"
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    "Description": "The ChromHeatMap package can be used to plot genome-wide data (e.g. expression, CGH, SNP) along each strand of a given chromosome as a heat map. The generated heat map can be used to interactively identify probes and genes of interest.",
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      "R (>= 2.8.0)",
      "Biobase (>= 2.1.0)",
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    "win64.binary.ver": "bin/windows64/contrib/2.12/RefPlus_1.20.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/RefPlus_1.20.0.tgz",
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    "Maintainer": "Kai-Ming Chang <kaiming@gmail.com>",
    "Author": "Kai-Ming Chang <kaiming@gmail.com>, Chris Harbron <Chris.Harbron@astrazeneca.com>, Marie C South <Marie.C.South@astrazeneca.com>",
    "Title": "A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods.",
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    "Suggests": [
      "affydata"
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    "License": "GPL (>= 2)",
    "biocViews": [
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      "OneChannel",
      "Preprocessing",
      "Software"
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    "Description": "The package contains functions for pre-processing Affymetrix data using the RMA+ and the RMA++ methods.",
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    "Depends": [
      "R (>= 2.10.0)",
      "R.utils"
    ],
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/DEGraph_1.0.0.tgz",
    "Version": "1.0.0",
    "Maintainer": "Laurent Jacob <laurent.jacob@gmail.com>",
    "Author": "Laurent Jacob, Pierre Neuvial and Sandrine Dudoit",
    "Title": "Two-sample tests on a graph",
    "source.ver": "src/contrib/DEGraph_1.0.0.tar.gz",
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      "graph",
      "KEGGgraph",
      "lattice",
      "mvtnorm",
      "R.methodsS3",
      "RBGL",
      "Rgraphviz",
      "rrcov"
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    "Suggests": [
      "corpcor",
      "fields",
      "graph",
      "KEGGgraph",
      "lattice",
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      "Rgraphviz"
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    "Package": "DEGraph",
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    "License": "GPL-3",
    "biocViews": [
      "Bioinformatics",
      "DifferentialExpression",
      "GraphsAndNetworks",
      "Microarray",
      "Software"
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    "Description": "DEGraph implements recent hypothesis testing methods which directly assess whether a particular gene network is differentially expressed between two conditions. This is to be contrasted with the more classical two-step approaches which first test individual genes, then test gene sets for enrichment in differentially expressed genes. These recent methods take into account the topology of the network to yield more powerful detection procedures. DEGraph provides methods to easily test all KEGG pathways for differential expression on any gene expression data set and tools to visualize the results.",
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      "R (>= 2.6.0)",
      "methods",
      "graph"
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    "URL": "http://www.bioconductor.org",
    "Maintainer": "VJ Carey <stvjc@channing.harvard.edu>",
    "Author": "VJ Carey <stvjc@channing.harvard.edu>",
    "Title": "interface to redland RDF utilities",
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    "Package": "Rredland",
    "vignettes": [
      "vignettes/Rredland/inst/doc/Rredland.pdf"
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    "License": "LGPL-2.1",
    "biocViews": [
      "Infrastructure",
      "Software"
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    "Description": "interface to redland RDF utilities; assumes librdf, possibly berkeley DB; include OWL files from www.biopax.org, and RDF serializations of various resources from ISB-SIB.CH; redland is a production of Dave Beckett (see librdf.org)"
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      "Biobase"
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    "Version": "1.10.0",
    "Maintainer": "Assaf Oron <assaf@uw.edu>",
    "Author": "Assaf Oron, Robert Gentleman (with contributions from S. Falcon and Z. Jiang)",
    "Title": "Linear Model Toolset for Gene Set Enrichment Analysis",
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    "Suggests": [
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      "Category",
      "multtest",
      "ALL",
      "annotate",
      "hgu95av2.db",
      "genefilter",
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    "Package": "GSEAlm",
    "vignettes": [
      "vignettes/GSEAlm/inst/doc/GSEAlm.pdf"
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    "License": "Artistic-2.0",
    "biocViews": [
      "Bioinformatics",
      "Microarray",
      "Software"
    ],
    "Description": "Models and methods for fitting linear models to gene expression data, together with tools for computing and using various regression diagnostics.",
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      "attract"
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    "win.binary.ver": "bin/windows/contrib/2.12/GSEAlm_1.10.0.zip"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/makePlatformDesign_1.14.0.zip",
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    "Version": "1.14.0",
    "Maintainer": "Benilton Carvalho <carvalho@bclab.org>",
    "Author": "Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber",
    "Title": "Platform Design Package",
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    "Imports": [
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      "affyio",
      "methods",
      "stats",
      "utils",
      "oligo"
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    "Package": "makePlatformDesign",
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    "License": "LGPL (>= 2)",
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      "Microarray",
      "OneChannel",
      "Preprocessing",
      "Software",
      "TwoChannel"
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    "Description": "makePlatformDesign creates the Platform Design environments (PDenvs) required by oligo.",
    "win.binary.ver": "bin/windows/contrib/2.12/makePlatformDesign_1.14.0.zip"
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  "microRNA": {
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/microRNA_1.8.0.tgz",
    "Version": "1.8.0",
    "Maintainer": "Chao-Jen Wong <cwon2@fhcrc.org>",
    "Author": "R. Gentleman, S. Falcon",
    "Title": "Data and functions for dealing with microRNAs",
    "suggestsMe": [
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    "Suggests": [
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    "Package": "microRNA",
    "License": "Artistic-2.0",
    "biocViews": [
      "Infrastructure",
      "SequenceAnnotation",
      "SequenceMatching",
      "Software"
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    "Description": "Different data resources for microRNAs and some functions for manipulating them.",
    "Enhances": [
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    "win.binary.ver": "bin/windows/contrib/2.12/microRNA_1.8.0.zip"
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      "R (>= 1.8.0)",
      "methods",
      "stats"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/externalVector_1.16.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/externalVector_1.16.0.tgz",
    "Version": "1.16.0",
    "Maintainer": "Biocore Team c/o BioC user list <bioconductor@stat.math.ethz.ch>",
    "Author": "Saikat DebRoy",
    "Title": "Vector objects for R with external storage",
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    "Package": "externalVector",
    "Archs": "i386, x64",
    "License": "LGPL",
    "biocViews": [
      "Infrastructure",
      "Software"
    ],
    "Description": "Basic class definitions and generics for external pointer based vector objects for R.  A simple in-memory implementation is also provided.",
    "win.binary.ver": "bin/windows/contrib/2.12/externalVector_1.16.0.zip"
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      "R(>= 2.2.0)",
      "marray"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/nnNorm_2.14.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/nnNorm_2.14.0.tgz",
    "Version": "2.14.0",
    "URL": "http://bioinformaticsprb.med.wayne.edu/tarca/",
    "Maintainer": "Adi Laurentiu Tarca <atarca@med.wayne.edu>",
    "Author": "Adi Laurentiu Tarca <atarca@med.wayne.edu>",
    "Title": "Spatial and intensity based normalization of cDNA microarray data based on robust neural nets",
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    "Imports": [
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      "grDevices",
      "marray",
      "methods",
      "nnet",
      "stats"
    ],
    "Package": "nnNorm",
    "vignettes": [
      "vignettes/nnNorm/inst/doc/nnNorm.pdf",
      "vignettes/nnNorm/inst/doc/nnNormGuide.pdf"
    ],
    "License": "LGPL",
    "biocViews": [
      "Microarray",
      "Preprocessing",
      "Software",
      "TwoChannel"
    ],
    "Description": "This package allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting.",
    "win.binary.ver": "bin/windows/contrib/2.12/nnNorm_2.14.0.zip"
  },
  "frma": {
    "Depends": [
      "R (>= 2.10.0)",
      "Biobase (>= 2.6.0)",
      "affyPLM (>= 1.22.0)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/frma_1.2.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/frma_1.2.0.tgz",
    "Version": "1.2.0",
    "URL": "http://bioconductor.org",
    "Maintainer": "Matthew N. McCall <mmccall@jhsph.edu>",
    "Author": "Matthew N. McCall <mmccall@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu>",
    "Title": "Frozen RMA and Barcode",
    "suggestsMe": [
      "frmaTools"
    ],
    "source.ver": "src/contrib/frma_1.2.0.tar.gz",
    "Imports": [
      "Biobase",
      "MASS",
      "affy",
      "affyPLM",
      "methods",
      "preprocessCore",
      "utils"
    ],
    "Suggests": [
      "hgu133afrmavecs",
      "hgu133abarcodevecs",
      "frmaExampleData"
    ],
    "Package": "frma",
    "vignettes": [
      "vignettes/frma/inst/doc/frma.pdf"
    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "Microarray",
      "Preprocessing",
      "Software"
    ],
    "Description": "Preprocessing and analysis for single microarrays and microarray batches.",
    "win.binary.ver": "bin/windows/contrib/2.12/frma_1.2.0.zip"
  },
  "OrderedList": {
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      "R (>= 2.1.0)",
      "Biobase (>= 1.5.12)",
      "twilight (>= 1.9.2)",
      "methods"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/OrderedList_1.22.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/OrderedList_1.22.0.tgz",
    "Version": "1.22.0",
    "URL": "http://compdiag.molgen.mpg.de/software/index.shtml",
    "Maintainer": "Claudio Lottaz <Claudio.Lottaz@klinik.uni-regensburg.de>",
    "Author": "Xinan Yang, Stefanie Scheid, Claudio Lottaz",
    "Title": "Similarities of Ordered Gene Lists",
    "source.ver": "src/contrib/OrderedList_1.22.0.tar.gz",
    "Imports": [
      "Biobase",
      "graphics",
      "methods",
      "stats",
      "twilight"
    ],
    "Package": "OrderedList",
    "vignettes": [
      "vignettes/OrderedList/inst/doc/bcb_logo.pdf",
      "vignettes/OrderedList/inst/doc/tr_2006_01.pdf"
    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "DifferentialExpression",
      "Microarray",
      "MultipleComparisons",
      "Software"
    ],
    "Description": "Detection of similarities between ordered lists of genes. Thereby, either simple lists can be compared or gene expression data can be used to deduce the lists. Significance of similarities is evaluated by shuffling lists or by resampling in microarray data, respectively.",
    "win.binary.ver": "bin/windows/contrib/2.12/OrderedList_1.22.0.zip"
  },
  "flowMerge": {
    "Depends": [
      "flowClust",
      "flowCore",
      "methods",
      "snow"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/flowMerge_1.4.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/flowMerge_1.4.0.tgz",
    "Version": "1.4.0",
    "Maintainer": "Greg Finak <greg.finak@ircm.qc.ca>",
    "Author": "Greg Finak <greg.finak@ircm.qc.ca>, Raphael Gottardo <raphael.gottardo@ircm.qc.ca>",
    "Title": "Cluster Merging for Flow Cytometry Data",
    "source.ver": "src/contrib/flowMerge_1.4.0.tar.gz",
    "Imports": [
      "rrcov",
      "flowClust",
      "flowCore",
      "graphics",
      "methods",
      "rrcov",
      "stats",
      "utils"
    ],
    "Package": "flowMerge",
    "vignettes": [
      "vignettes/flowMerge/inst/doc/flowMerge.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "Bioinformatics",
      "Clustering",
      "FlowCytometry",
      "Software"
    ],
    "Description": "Merging of mixture components for model-based automated gating of flow cytometry data using the flowClust framework. Note: users should have a working copy of flowClust 2.0 installed.",
    "win.binary.ver": "bin/windows/contrib/2.12/flowMerge_1.4.0.zip"
  },
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      "R (>= 2.10.0)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/flowMeans_1.2.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/flowMeans_1.2.0.tgz",
    "Version": "1.2.0",
    "Maintainer": "Nima Aghaeepour <naghaeep@bccrc.ca>",
    "Author": "Nima Aghaeepour",
    "Title": "Non-parametric Flow Cytometry Data Gating",
    "source.ver": "src/contrib/flowMeans_1.2.0.tar.gz",
    "Imports": [
      "Biobase",
      "graphics",
      "grDevices",
      "methods",
      "rrcov",
      "stats",
      "feature",
      "flowCore"
    ],
    "Package": "flowMeans",
    "vignettes": [
      "vignettes/flowMeans/inst/doc/flowMeans.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "Bioinformatics",
      "Cancer",
      "CellBiology",
      "Clustering",
      "FlowCytData",
      "FlowCytometry",
      "HIV",
      "Software",
      "StemCells"
    ],
    "Description": "Identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection. Note: R 2.11.0 or newer is required.",
    "win.binary.ver": "bin/windows/contrib/2.12/flowMeans_1.2.0.zip"
  },
  "bridge": {
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      "R (>= 1.9.0)",
      "rama"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/bridge_1.14.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/bridge_1.14.0.tgz",
    "Version": "1.14.0",
    "Maintainer": "Raphael Gottardo <raph@stat.ubc.ca>",
    "Author": "Raphael Gottardo",
    "Title": "Bayesian Robust Inference for Differential Gene Expression",
    "source.ver": "src/contrib/bridge_1.14.0.tar.gz",
    "Package": "bridge",
    "vignettes": [
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    ],
    "Archs": "i386, x64",
    "License": "GPL (>= 2)",
    "biocViews": [
      "DifferentialExpression",
      "Microarray",
      "OneChannel",
      "Software",
      "TwoChannel"
    ],
    "Description": "Test for differentially expressed genes with microarray data. This package can be used with both cDNA microarrays or Affymetrix chip. The packge fits a robust Bayesian hierarchical model for testing for differential expression. Outliers are modeled explicitly using a $t$-distribution. The model includes an exchangeable prior for the variances which allow different variances for the genes but still shrink extreme empirical variances. Our model can be used for testing for differentially expressed genes among multiple samples, and can distinguish between the different possible patterns of differential expression when there are three or more samples. Parameter estimation is carried out using a novel version of Markov Chain Monte Carlo that is appropriate when the model puts mass on subspaces of the full parameter space.",
    "win.binary.ver": "bin/windows/contrib/2.12/bridge_1.14.0.zip"
  },
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      "R (>= 2.10.0)",
      "Biobase",
      "Biostrings",
      "BSgenome.Scerevisiae.UCSC.sacCer2"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/R453Plus1Toolbox_1.0.1.tgz",
    "Version": "1.0.1",
    "Maintainer": "H-U Klein <h.klein@uni-muenster.de>",
    "Author": "H-U Klein, C Bartenhagen, C Ruckert",
    "Title": "A package for importing and analyzing data from Roche's Genome Sequencer System.",
    "source.ver": "src/contrib/R453Plus1Toolbox_1.0.1.tar.gz",
    "Imports": [
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      "biomaRt",
      "Biostrings",
      "BSgenome",
      "IRanges",
      "methods",
      "R2HTML",
      "Rsamtools",
      "rtracklayer",
      "ShortRead"
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      "ShortRead",
      "Rsamtools",
      "BSgenome.Hsapiens.UCSC.hg19"
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    "Package": "R453Plus1Toolbox",
    "vignettes": [
      "vignettes/R453Plus1Toolbox/inst/doc/vignette.pdf"
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    "License": "LGPL-3",
    "biocViews": [
      "DataImport",
      "DataRepresentation",
      "HighThroughputSequencing",
      "Infrastructure",
      "QualityControl",
      "ReportWriting",
      "Software",
      "Visualization"
    ],
    "Description": "The R453Plus1 Toolbox comprises useful functions for the analysis of data generated by Roche's 454 sequencing platform. It adds functions for quality assurance as well as for annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. Further, a pipeline for the detection of structural variants is provided.",
    "win.binary.ver": "bin/windows/contrib/2.12/R453Plus1Toolbox_1.0.1.zip"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/splots_1.16.1.tgz",
    "Version": "1.16.1",
    "dependsOnMe": [
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    "Maintainer": "Wolfgang Huber <whuber@embl.de>",
    "Author": "Wolfgang Huber, Oleg Sklyar",
    "Title": "Visualization of high-throughput assays in microtitre plate or slide format",
    "source.ver": "src/contrib/splots_1.16.1.tar.gz",
    "Imports": [
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      "RColorBrewer"
    ],
    "Package": "splots",
    "vignettes": [
      "vignettes/splots/inst/doc/splotsHOWTO.pdf"
    ],
    "License": "LGPL",
    "biocViews": [
      "HighThroughputSequencing",
      "MicrotitrePlateAssay",
      "Software",
      "Visualization"
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    "win.binary.ver": "bin/windows/contrib/2.12/splots_1.16.1.zip"
  },
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      "methods",
      "utils",
      "Biobase (>= 1.17.0)"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/AnnotationDbi_1.12.1.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/AnnotationDbi_1.12.0.tgz",
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    "dependsOnMe": [
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      "agprobe",
      "annotate",
      "anopheles.db0",
      "arabidopsis.db0",
      "ath1121501.db",
      "ath1121501probe",
      "attract",
      "barley1probe",
      "bovine.db",
      "bovine.db0",
      "bovineprobe",
      "bsubtilisprobe",
      "canine.db",
      "canine.db0",
      "canine2.db",
      "canine2probe",
      "canineprobe",
      "Category",
      "celegans.db",
      "celegansprobe",
      "chicken.db",
      "chicken.db0",
      "chickenprobe",
      "chimp.db0",
      "ChromHeatMap",
      "citrusprobe",
      "cottonprobe",
      "DO.db",
      "drosgenome1.db",
      "drosgenome1probe",
      "drosophila2.db",
      "drosophila2probe",
      "ecoli2.db",
      "ecoli2probe",
      "ecoliasv2probe",
      "ecoliK12.db0",
      "ecoliprobe",
      "ecoliSakai.db0",
      "eisa",
      "fly.db0",
      "gahgu133a.db",
      "gahgu133aprobe",
      "gahgu133b.db",
      "gahgu133bprobe",
      "gahgu133plus2.db",
      "gahgu133plus2probe",
      "gahgu95av2.db",
      "gahgu95av2probe",
      "gahgu95b.db",
      "gahgu95bprobe",
      "gahgu95c.db",
      "gahgu95cprobe",
      "gahgu95d.db",
      "gahgu95dprobe",
      "gahgu95e.db",
      "gahgu95eprobe",
      "gene2pathway",
      "GGdata",
      "GGHumanMethCancerPanelv1.db",
      "GO.db",
      "goProfiles",
      "GOSemSim",
      "h10kcod.db",
      "h20kcod.db",
      "hcg110.db",
      "hcg110probe",
      "hgfocus.db",
      "hgfocusprobe",
      "hgu133a.db",
      "hgu133a2.db",
      "hgu133a2probe",
      "hgu133aprobe",
      "hgu133atagprobe",
      "hgu133b.db",
      "hgu133bprobe",
      "hgu133plus2.db",
      "hgu133plus2probe",
      "hgu219.db",
      "hgu219probe",
      "hgu95a.db",
      "hgu95aprobe",
      "hgu95av2.db",
      "hgu95av2probe",
      "hgu95b.db",
      "hgu95bprobe",
      "hgu95c.db",
      "hgu95cprobe",
      "hgu95d.db",
      "hgu95dprobe",
      "hgu95e.db",
      "hgu95eprobe",
      "hguatlas13k.db",
      "hgubeta7.db",
      "hguDKFZ31.db",
      "hgug4100a.db",
      "hgug4101a.db",
      "hgug4110b.db",
      "hgug4111a.db",
      "hgug4112a.db",
      "hguqiagenv3.db",
      "hi16cod.db",
      "hom.At.inp.db",
      "hom.Ce.inp.db",
      "hom.Dm.inp.db",
      "hom.Dr.inp.db",
      "hom.Hs.inp.db",
      "hom.Mm.inp.db",
      "hom.Rn.inp.db",
      "hom.Sc.inp.db",
      "hs25kresogen.db",
      "Hs6UG171.db",
      "HsAgilentDesign026652.db",
      "hthgu133a.db",
      "hthgu133aprobe",
      "hthgu133b.db",
      "hthgu133bprobe",
      "hthgu133pluspmprobe",
      "htmg430aprobe",
      "htmg430bprobe",
      "htmg430pmprobe",
      "htrat230pmprobe",
      "htratfocusprobe",
      "hu35ksuba.db",
      "hu35ksubaprobe",
      "hu35ksubb.db",
      "hu35ksubbprobe",
      "hu35ksubc.db",
      "hu35ksubcprobe",
      "hu35ksubd.db",
      "hu35ksubdprobe",
      "hu6800.db",
      "hu6800probe",
      "HuExExonProbesetLocationHg18",
      "HuExExonProbesetLocationHg19",
      "hugene10stprobeset.db",
      "hugene10sttranscriptcluster.db",
      "hugene10stv1probe",
      "hugene11stprobeset.db",
      "hugene11sttranscriptcluster.db",
      "human.db0",
      "HuO22.db",
      "hwgcod.db",
      "illuminaHumanDASLBeadID.db",
      "IlluminaHumanMethylation27k.db",
      "illuminaHumanv1.db",
      "illuminaHumanv1BeadID.db",
      "illuminaHumanv2.db",
      "illuminaHumanv2BeadID.db",
      "illuminaHumanv3.db",
      "illuminaHumanv3BeadID.db",
      "illuminaHumanv4.db",
      "illuminaHumanv4BeadID.db",
      "illuminaMousev1.db",
      "illuminaMousev1BeadID.db",
      "illuminaMousev1p1.db",
      "illuminaMousev1p1BeadID.db",
      "illuminaMousev2.db",
      "illuminaMousev2BeadID.db",
      "illuminaRatv1.db",
      "illuminaRatv1BeadID.db",
      "indac.db",
      "JazaeriMetaData.db",
      "KEGG.db",
      "LAPOINTE.db",
      "lumiHumanAll.db",
      "lumiHumanIDMapping",
      "lumiMouseAll.db",
      "lumiMouseIDMapping",
      "lumiRatAll.db",
      "lumiRatIDMapping",
      "m10kcod.db",
      "m20kcod.db",
      "maizeprobe",
      "malaria.db0",
      "medicagoprobe",
      "mgu74a.db",
      "mgu74aprobe",
      "mgu74av2.db",
      "mgu74av2probe",
      "mgu74b.db",
      "mgu74bprobe",
      "mgu74bv2.db",
      "mgu74bv2probe",
      "mgu74c.db",
      "mgu74cprobe",
      "mgu74cv2.db",
      "mgu74cv2probe",
      "mguatlas5k.db",
      "mgug4104a.db",
      "mgug4120a.db",
      "mgug4121a.db",
      "mgug4122a.db",
      "mi16cod.db",
      "mirbase.db",
      "mirna10probe",
      "mm24kresogen.db",
      "MmAgilentDesign026655.db",
      "moe430a.db",
      "moe430aprobe",
      "moe430b.db",
      "moe430bprobe",
      "MoExExonProbesetLocation",
      "mogene10stprobeset.db",
      "mogene10sttranscriptcluster.db",
      "mogene10stv1probe",
      "mogene11stprobeset.db",
      "mogene11sttranscriptcluster.db",
      "mouse.db0",
      "mouse4302.db",
      "mouse4302probe",
      "mouse430a2.db",
      "mouse430a2probe",
      "mpedbarray.db",
      "mu11ksuba.db",
      "mu11ksubaprobe",
      "mu11ksubb.db",
      "mu11ksubbprobe",
      "Mu15v1.db",
      "mu19ksuba.db",
      "mu19ksubb.db",
      "mu19ksubc.db",
      "Mu22v3.db",
      "mwgcod.db",
      "Norway981.db",
      "nugohs1a520180.db",
      "nugohs1a520180probe",
      "nugomm1a520177.db",
      "nugomm1a520177probe",
      "oneChannelGUI",
      "ontoTools",
      "OperonHumanV3.db",
      "org.Ag.eg.db",
      "org.At.tair.db",
      "org.Bt.eg.db",
      "org.Ce.eg.db",
      "org.Cf.eg.db",
      "org.Dm.eg.db",
      "org.Dr.eg.db",
      "org.EcK12.eg.db",
      "org.EcSakai.eg.db",
      "org.Gg.eg.db",
      "org.Hs.eg.db",
      "org.Hs.ipi.db",
      "org.Mm.eg.db",
      "org.Mmu.eg.db",
      "org.Pf.plasmo.db",
      "org.Pt.eg.db",
      "org.Rn.eg.db",
      "org.Sc.sgd.db",
      "org.Sco.eg.db",
      "org.Ss.eg.db",
      "org.Xl.eg.db",
      "paeg1aprobe",
      "PAnnBuilder",
      "PartheenMetaData.db",
      "pathRender",
      "pedbarrayv10.db",
      "pedbarrayv9.db",
      "PFAM.db",
      "PGSEA",
      "pig.db0",
      "plasmodiumanophelesprobe",
      "POCRCannotation.db",
      "poplarprobe",
      "porcine.db",
      "porcineprobe",
      "r10kcod.db",
      "rae230a.db",
      "rae230aprobe",
      "rae230b.db",
      "rae230bprobe",
      "RaExExonProbesetLocation",
      "ragene10stprobeset.db",
      "ragene10sttranscriptcluster.db",
      "ragene10stv1probe",
      "ragene11stprobeset.db",
      "ragene11sttranscriptcluster.db",
      "rat.db0",
      "rat2302.db",
      "rat2302probe",
      "rattoxfxprobe",
      "Resourcerer",
      "rgu34a.db",
      "rgu34aprobe",
      "rgu34b.db",
      "rgu34bprobe",
      "rgu34c.db",
      "rgu34cprobe",
      "rguatlas4k.db",
      "rgug4105a.db",
      "rgug4130a.db",
      "rgug4131a.db",
      "rhesus.db0",
      "rhesusprobe",
      "ri16cod.db",
      "riceprobe",
      "RnAgilentDesign028282.db",
      "rnu34.db",
      "rnu34probe",
      "Roberts2005Annotation.db",
      "RpsiXML",
      "rtu34.db",
      "rtu34probe",
      "rwgcod.db",
      "saureusprobe",
      "SHDZ.db",
      "soybeanprobe",
      "sugarcaneprobe",
      "targetscan.Hs.eg.db",
      "targetscan.Mm.eg.db",
      "test3probe",
      "tomatoprobe",
      "topGO",
      "u133x3p.db",
      "u133x3pprobe",
      "vitisviniferaprobe",
      "wheatprobe",
      "worm.db0",
      "xenopus.db0",
      "xenopuslaevisprobe",
      "xlaevis.db",
      "xlaevis2probe",
      "xtropicalisprobe",
      "yeast.db0",
      "yeast2.db",
      "yeast2probe",
      "ygs98.db",
      "ygs98probe",
      "zebrafish.db",
      "zebrafish.db0",
      "zebrafishprobe"
    ],
    "Maintainer": "Biocore Team c/o BioC user list <bioconductor@stat.math.ethz.ch>",
    "Author": "Herve Pages, Marc Carlson, Seth Falcon, Nianhua Li",
    "Title": "Annotation Database Interface",
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      "GeneAnswers",
      "GeneRegionScan",
      "sigPathway"
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      "utils",
      "Biobase",
      "DBI",
      "RSQLite"
    ],
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      "RSQLite (>= 0.6-4)",
      "hgu95av2.db",
      "GO.db",
      "human.db0",
      "hgu95av2cdf",
      "affy",
      "KEGG.db"
    ],
    "Package": "AnnotationDbi",
    "vignettes": [
      "vignettes/AnnotationDbi/inst/doc/AnnotationDbi.pdf",
      "vignettes/AnnotationDbi/inst/doc/makeProbePackage.pdf",
      "vignettes/AnnotationDbi/inst/doc/NewSchema.pdf",
      "vignettes/AnnotationDbi/inst/doc/SQLForge.pdf"
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      "affycoretools",
      "ag.db",
      "annaffy",
      "annotate",
      "anopheles.db0",
      "arabidopsis.db0",
      "ath1121501.db",
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      "bovine.db0",
      "canine.db",
      "canine.db0",
      "canine2.db",
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      "celegans.db",
      "chicken.db",
      "chicken.db0",
      "chimp.db0",
      "ChromHeatMap",
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      "DO.db",
      "domainsignatures",
      "drosgenome1.db",
      "drosophila2.db",
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      "ecoliSakai.db0",
      "ExpressionView",
      "fly.db0",
      "gahgu133a.db",
      "gahgu133b.db",
      "gahgu133plus2.db",
      "gahgu95av2.db",
      "gahgu95b.db",
      "gahgu95c.db",
      "gahgu95d.db",
      "gahgu95e.db",
      "genefilter",
      "geneplotter",
      "GGBase",
      "GGHumanMethCancerPanelv1.db",
      "GGtools",
      "GlobalAncova",
      "globaltest",
      "GO.db",
      "goseq",
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      "GSEABase",
      "h10kcod.db",
      "h20kcod.db",
      "hcg110.db",
      "hgfocus.db",
      "hgu133a.db",
      "hgu133a2.db",
      "hgu133b.db",
      "hgu133plus2.db",
      "hgu219.db",
      "hgu95a.db",
      "hgu95av2.db",
      "hgu95b.db",
      "hgu95c.db",
      "hgu95d.db",
      "hgu95e.db",
      "hguatlas13k.db",
      "hgubeta7.db",
      "hguDKFZ31.db",
      "hgug4100a.db",
      "hgug4101a.db",
      "hgug4110b.db",
      "hgug4111a.db",
      "hgug4112a.db",
      "hguqiagenv3.db",
      "hi16cod.db",
      "hom.At.inp.db",
      "hom.Ce.inp.db",
      "hom.Dm.inp.db",
      "hom.Dr.inp.db",
      "hom.Hs.inp.db",
      "hom.Mm.inp.db",
      "hom.Rn.inp.db",
      "hom.Sc.inp.db",
      "hs25kresogen.db",
      "Hs6UG171.db",
      "HsAgilentDesign026652.db",
      "hthgu133a.db",
      "hthgu133b.db",
      "HTSanalyzeR",
      "hu35ksuba.db",
      "hu35ksubb.db",
      "hu35ksubc.db",
      "hu35ksubd.db",
      "hu6800.db",
      "hugene10stprobeset.db",
      "hugene10sttranscriptcluster.db",
      "hugene11stprobeset.db",
      "hugene11sttranscriptcluster.db",
      "human.db0",
      "HuO22.db",
      "hwgcod.db",
      "illuminaHumanDASLBeadID.db",
      "IlluminaHumanMethylation27k.db",
      "illuminaHumanv1.db",
      "illuminaHumanv1BeadID.db",
      "illuminaHumanv2.db",
      "illuminaHumanv2BeadID.db",
      "illuminaHumanv3.db",
      "illuminaHumanv3BeadID.db",
      "illuminaHumanv4.db",
      "illuminaHumanv4BeadID.db",
      "illuminaMousev1.db",
      "illuminaMousev1BeadID.db",
      "illuminaMousev1p1.db",
      "illuminaMousev1p1BeadID.db",
      "illuminaMousev2.db",
      "illuminaMousev2BeadID.db",
      "illuminaRatv1.db",
      "illuminaRatv1BeadID.db",
      "indac.db",
      "JazaeriMetaData.db",
      "KEGG.db",
      "keggorthology",
      "LAPOINTE.db",
      "lumi",
      "lumiHumanAll.db",
      "lumiHumanIDMapping",
      "lumiMouseAll.db",
      "lumiMouseIDMapping",
      "lumiRatAll.db",
      "lumiRatIDMapping",
      "m10kcod.db",
      "m20kcod.db",
      "malaria.db0",
      "mgu74a.db",
      "mgu74av2.db",
      "mgu74b.db",
      "mgu74bv2.db",
      "mgu74c.db",
      "mgu74cv2.db",
      "mguatlas5k.db",
      "mgug4104a.db",
      "mgug4120a.db",
      "mgug4121a.db",
      "mgug4122a.db",
      "mi16cod.db",
      "mirbase.db",
      "mm24kresogen.db",
      "MmAgilentDesign026655.db",
      "moe430a.db",
      "moe430b.db",
      "mogene10stprobeset.db",
      "mogene10sttranscriptcluster.db",
      "mogene11stprobeset.db",
      "mogene11sttranscriptcluster.db",
      "mouse.db0",
      "mouse4302.db",
      "mouse430a2.db",
      "mpedbarray.db",
      "mu11ksuba.db",
      "mu11ksubb.db",
      "Mu15v1.db",
      "mu19ksuba.db",
      "mu19ksubb.db",
      "mu19ksubc.db",
      "Mu22v3.db",
      "mwgcod.db",
      "Norway981.db",
      "nugohs1a520180.db",
      "nugomm1a520177.db",
      "OperonHumanV3.db",
      "org.Ag.eg.db",
      "org.At.tair.db",
      "org.Bt.eg.db",
      "org.Ce.eg.db",
      "org.Cf.eg.db",
      "org.Dm.eg.db",
      "org.Dr.eg.db",
      "org.EcK12.eg.db",
      "org.EcSakai.eg.db",
      "org.Gg.eg.db",
      "org.Hs.eg.db",
      "org.Hs.ipi.db",
      "org.Mm.eg.db",
      "org.Mmu.eg.db",
      "org.Pf.plasmo.db",
      "org.Pt.eg.db",
      "org.Rn.eg.db",
      "org.Sc.sgd.db",
      "org.Sco.eg.db",
      "org.Ss.eg.db",
      "org.Xl.eg.db",
      "PAnnBuilder",
      "PartheenMetaData.db",
      "PatientGeneSets",
      "PCpheno",
      "pedbarrayv10.db",
      "pedbarrayv9.db",
      "PFAM.db",
      "pig.db0",
      "POCRCannotation.db",
      "porcine.db",
      "qpgraph",
      "r10kcod.db",
      "rae230a.db",
      "rae230b.db",
      "ragene10stprobeset.db",
      "ragene10sttranscriptcluster.db",
      "ragene11stprobeset.db",
      "ragene11sttranscriptcluster.db",
      "rat.db0",
      "rat2302.db",
      "rgu34a.db",
      "rgu34b.db",
      "rgu34c.db",
      "rguatlas4k.db",
      "rgug4105a.db",
      "rgug4130a.db",
      "rgug4131a.db",
      "rhesus.db0",
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      "RmiR.Hs.miRNA",
      "RmiR.hsa",
      "RnAgilentDesign028282.db",
      "rnu34.db",
      "Roberts2005Annotation.db",
      "rtu34.db",
      "rwgcod.db",
      "safe",
      "ScISI",
      "SHDZ.db",
      "SLGI",
      "targetscan.Hs.eg.db",
      "targetscan.Mm.eg.db",
      "tigre",
      "topGO",
      "u133x3p.db",
      "worm.db0",
      "xenopus.db0",
      "xlaevis.db",
      "yeast.db0",
      "yeast2.db",
      "ygs98.db",
      "zebrafish.db",
      "zebrafish.db0"
    ],
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  },
  "mdqc": {
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      "cluster",
      "MASS"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/mdqc_1.12.1.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/mdqc_1.12.1.tgz",
    "Version": "1.12.1",
    "Maintainer": "Gabriela Cohen-Freue <gcohen@mrl.ubc.ca>",
    "Author": "Justin Harrington",
    "Title": "Mahalanobis Distance Quality Control for microarrays",
    "source.ver": "src/contrib/mdqc_1.12.1.tar.gz",
    "Package": "mdqc",
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    ],
    "License": "LGPL (>= 2)",
    "biocViews": [
      "Software"
    ],
    "Description": "MDQC is a multivariate quality assessment method for microarrays based on quality control (QC) reports. The Mahalanobis distance of an array's quality attributes is used to measure the similarity of the quality of that array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality.",
    "importsMe": [
      "arrayMvout"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/mdqc_1.12.1.zip"
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      "methods",
      "IRanges (>= 1.7.7)",
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      "Biostrings (>= 2.17.5)"
    ],
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/BSgenome_1.18.3.tgz",
    "Version": "1.18.3",
    "dependsOnMe": [
      "BSgenome.Amellifera.BeeBase.assembly4",
      "BSgenome.Amellifera.UCSC.apiMel2",
      "BSgenome.Athaliana.TAIR.01222004",
      "BSgenome.Athaliana.TAIR.04232008",
      "BSgenome.Athaliana.TAIR.TAIR9",
      "BSgenome.Btaurus.UCSC.bosTau3",
      "BSgenome.Btaurus.UCSC.bosTau4",
      "BSgenome.Celegans.UCSC.ce2",
      "BSgenome.Celegans.UCSC.ce6",
      "BSgenome.Cfamiliaris.UCSC.canFam2",
      "BSgenome.Dmelanogaster.UCSC.dm2",
      "BSgenome.Dmelanogaster.UCSC.dm3",
      "BSgenome.Drerio.UCSC.danRer5",
      "BSgenome.Drerio.UCSC.danRer6",
      "BSgenome.Ecoli.NCBI.20080805",
      "BSgenome.Gaculeatus.UCSC.gasAcu1",
      "BSgenome.Ggallus.UCSC.galGal3",
      "BSgenome.Hsapiens.UCSC.hg17",
      "BSgenome.Hsapiens.UCSC.hg18",
      "BSgenome.Hsapiens.UCSC.hg19",
      "BSgenome.Mmusculus.UCSC.mm8",
      "BSgenome.Mmusculus.UCSC.mm9",
      "BSgenome.Ptroglodytes.UCSC.panTro2",
      "BSgenome.Rnorvegicus.UCSC.rn4",
      "BSgenome.Scerevisiae.UCSC.sacCer1",
      "BSgenome.Scerevisiae.UCSC.sacCer2",
      "ChIPpeakAnno",
      "chipseq",
      "leeBamViews",
      "MEDIPS",
      "PICS",
      "rGADEM"
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    "Maintainer": "H. Pages <hpages@fhcrc.org>",
    "Author": "Herve Pages",
    "Title": "Infrastructure for Biostrings-based genome data packages",
    "suggestsMe": [
      "Biostrings",
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      "GenomicRanges",
      "MEDIPS",
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      "SNPlocs.Hsapiens.dbSNP.20090506",
      "SNPlocs.Hsapiens.dbSNP.20100427",
      "SNPlocs.Hsapiens.dbSNP.20101109"
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    "source.ver": "src/contrib/BSgenome_1.18.3.tar.gz",
    "Suggests": [
      "RUnit",
      "BSgenome.Celegans.UCSC.ce2 (>= 1.3.11)",
      "BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.11)",
      "SNPlocs.Hsapiens.dbSNP.20100427",
      "hgu95av2probe",
      "Biobase"
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    "Package": "BSgenome",
    "vignettes": [
      "vignettes/BSgenome/inst/doc/BSgenomeForge.pdf",
      "vignettes/BSgenome/inst/doc/GenomeSearching.pdf"
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    "License": "Artistic-2.0",
    "biocViews": [
      "Annotation",
      "DataRepresentation",
      "Genetics",
      "Infrastructure",
      "SNP",
      "SequenceMatching",
      "Software"
    ],
    "Description": "Infrastructure shared by all the Biostrings-based genome data packages",
    "importsMe": [
      "BSgenome.Amellifera.BeeBase.assembly4",
      "BSgenome.Amellifera.UCSC.apiMel2",
      "BSgenome.Athaliana.TAIR.01222004",
      "BSgenome.Athaliana.TAIR.04232008",
      "BSgenome.Athaliana.TAIR.TAIR9",
      "BSgenome.Btaurus.UCSC.bosTau3",
      "BSgenome.Btaurus.UCSC.bosTau4",
      "BSgenome.Celegans.UCSC.ce2",
      "BSgenome.Celegans.UCSC.ce6",
      "BSgenome.Cfamiliaris.UCSC.canFam2",
      "BSgenome.Dmelanogaster.UCSC.dm2",
      "BSgenome.Dmelanogaster.UCSC.dm3",
      "BSgenome.Drerio.UCSC.danRer5",
      "BSgenome.Drerio.UCSC.danRer6",
      "BSgenome.Ecoli.NCBI.20080805",
      "BSgenome.Gaculeatus.UCSC.gasAcu1",
      "BSgenome.Ggallus.UCSC.galGal3",
      "BSgenome.Hsapiens.UCSC.hg17",
      "BSgenome.Hsapiens.UCSC.hg18",
      "BSgenome.Hsapiens.UCSC.hg19",
      "BSgenome.Mmusculus.UCSC.mm8",
      "BSgenome.Mmusculus.UCSC.mm9",
      "BSgenome.Ptroglodytes.UCSC.panTro2",
      "BSgenome.Rnorvegicus.UCSC.rn4",
      "BSgenome.Scerevisiae.UCSC.sacCer1",
      "BSgenome.Scerevisiae.UCSC.sacCer2",
      "charm",
      "ChIPpeakAnno",
      "chipseq",
      "girafe",
      "MEDIPS",
      "PICS",
      "R453Plus1Toolbox",
      "rtracklayer"
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    "win.binary.ver": "bin/windows/contrib/2.12/BSgenome_1.18.3.zip"
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    "Depends": [
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/TypeInfo_1.16.0.zip",
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    "Maintainer": "Duncan Temple Lang <duncan@wald.ucdavis.edu>",
    "Author": "Duncan Temple Lang Robert Gentleman (<rgentlem@fhcrc.org>)",
    "Title": "Optional Type Specification Prototype",
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    "Package": "TypeInfo",
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    ],
    "License": "BSD",
    "biocViews": [
      "Infrastructure",
      "Software"
    ],
    "Description": "A prototype for a mechanism for specifying the types of parameters and the return value for an R function. This is meta-information that can be used to generate stubs for servers and various interfaces to these functions. Additionally, the arguments in a call to a typed function can be validated using the type specifications. We allow types to be specified as either i) by class name using either inheritance - is(x, className), or strict instance of - class(x) %in% className, or ii) a dynamic test given as an R expression which is evaluated at run-time. More precise information and interesting tests can be done via ii), but it is harder to use this information as meta-data as it requires more effort to interpret it and it is of course run-time information. It is typically more meaningful.",
    "win.binary.ver": "bin/windows/contrib/2.12/TypeInfo_1.16.0.zip"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/gpls_1.22.0.tgz",
    "Version": "1.22.0",
    "Maintainer": "Biocore Team c/o BioC user list <bioconductor@stat.math.ethz.ch>",
    "Author": "Beiying Ding",
    "Title": "Classification using generalized partial least squares",
    "suggestsMe": [
      "MCRestimate",
      "MLInterfaces"
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    "source.ver": "src/contrib/gpls_1.22.0.tar.gz",
    "Imports": [
      "stats"
    ],
    "Package": "gpls",
    "vignettes": [
      "vignettes/gpls/inst/doc/gpls.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "Bioinformatics",
      "Classification",
      "Microarray",
      "Software"
    ],
    "Description": "Classification using generalized partial least squares for two-group and multi-group (more than 2 group) classification.",
    "win.binary.ver": "bin/windows/contrib/2.12/gpls_1.22.0.zip"
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  "flowFP": {
    "Depends": [
      "R(>= 2.5.0)",
      "flowCore",
      "flowViz"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/flowFP_1.6.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/flowFP_1.6.0.tgz",
    "Version": "1.6.0",
    "Maintainer": "Herb Holyst <holyst@mail.med.upenn.edu>",
    "Author": "Herb Holyst <holyst@mail.med.upenn.edu>, Wade Rogers <rogersw@mail.med.upenn.edu>",
    "Title": "Fingerprinting for Flow Cytometry",
    "source.ver": "src/contrib/flowFP_1.6.0.tar.gz",
    "Imports": [
      "Biobase",
      "flowCore",
      "flowViz",
      "graphics",
      "grDevices",
      "methods",
      "stats"
    ],
    "Package": "flowFP",
    "vignettes": [
      "vignettes/flowFP/inst/doc/flowFP_HowTo.pdf"
    ],
    "Archs": "i386, x64",
    "License": "Artistic-2.0",
    "biocViews": [
      "Bioinformatics",
      "CellBasedAssays",
      "Clustering",
      "Flowcytometry",
      "Software",
      "Visualization"
    ],
    "Description": "Fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and datamining tools for flow cytometry.",
    "win.binary.ver": "bin/windows/contrib/2.12/flowFP_1.6.0.zip"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/ABarray_1.18.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/ABarray_1.18.0.tgz",
    "Version": "1.18.0",
    "Maintainer": "Yongming Andrew Sun <sunya@appliedbiosystems.com>",
    "Author": "Yongming Andrew Sun",
    "Title": "Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Micorarray (AB1700) gene expression data.",
    "source.ver": "src/contrib/ABarray_1.18.0.tar.gz",
    "Imports": [
      "Biobase",
      "graphics",
      "grDevices",
      "methods",
      "multtest",
      "stats",
      "tcltk",
      "utils"
    ],
    "Suggests": [
      "limma",
      "LPE"
    ],
    "Package": "ABarray",
    "vignettes": [
      "vignettes/ABarray/inst/doc/ABarray.pdf",
      "vignettes/ABarray/inst/doc/ABarrayGUI.pdf"
    ],
    "License": "GPL",
    "biocViews": [
      "Microarray",
      "OneChannel",
      "Preprocessing",
      "Software"
    ],
    "Description": "Automated pipline to perform gene expression analysis for Applied Biosystems Genome Survey Microarray (AB1700) data format. Functions include data preprocessing, filtering, control probe analysis, statistical analysis in one single function. A GUI interface is also provided. The raw data, processed data, graphics output and statistical results are organized into folders according to the analysis settings used.",
    "win.binary.ver": "bin/windows/contrib/2.12/ABarray_1.18.0.zip"
  },
  "RBioinf": {
    "Depends": [
      "graph",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/RBioinf_1.10.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/RBioinf_1.10.0.tgz",
    "Version": "1.10.0",
    "Maintainer": "Robert Gentleman <rgentlem@gmail.com>",
    "Author": "Robert Gentleman",
    "Title": "RBioinf",
    "source.ver": "src/contrib/RBioinf_1.10.0.tar.gz",
    "Package": "RBioinf",
    "vignettes": [
      "vignettes/RBioinf/inst/doc/RBioinf.pdf"
    ],
    "Archs": "i386, x64",
    "License": "Artistic-2.0",
    "biocViews": [
      "Annotation",
      "Classification",
      "Clustering",
      "GeneExpression",
      "Microarray",
      "MultipleComparison",
      "Preprocessing",
      "QualityControl",
      "Software"
    ],
    "Description": "Functions and datasets and examples to accompany the monograph R For Bioinformatics.",
    "win.binary.ver": "bin/windows/contrib/2.12/RBioinf_1.10.0.zip"
  },
  "SpeCond": {
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      "R (>= 2.10.0)",
      "mclust (>= 3.3.1)",
      "Biobase (>= 1.15.13)",
      "fields",
      "hwriter (>= 1.1)",
      "RColorBrewer",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/SpeCond_1.4.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/SpeCond_1.4.0.tgz",
    "Version": "1.4.0",
    "Maintainer": "Florence Cavalli <florence@ebi.ac.uk>",
    "Author": "Florence Cavalli",
    "Title": "Condition specific detection from expression data",
    "source.ver": "src/contrib/SpeCond_1.4.0.tar.gz",
    "Package": "SpeCond",
    "vignettes": [
      "vignettes/SpeCond/inst/doc/SpeCond.pdf"
    ],
    "License": "LGPL (>=2)",
    "biocViews": [
      "Bioinformatics",
      "Clustering",
      "DifferentialExpression",
      "Microarray",
      "MultipleComparisons",
      "ReportWriting",
      "Software"
    ],
    "Description": "This package performs a gene expression data analysis to detect condition-specific genes. Such genes are significantly up- or down-regulated in a small number of conditions. It does so by fitting a mixture of normal distributions to the expression values. Conditions can be environmental conditions, different tissues, organs or any other sources that you wish to compare in terms of gene expression.",
    "win.binary.ver": "bin/windows/contrib/2.12/SpeCond_1.4.0.zip"
  },
  "PCpheno": {
    "Depends": [
      "Category",
      "ScISI (>= 1.3.0)",
      "SLGI",
      "ppiStats",
      "ppiData",
      "annotate (>= 1.17.4)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/PCpheno_1.12.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/PCpheno_1.12.0.tgz",
    "Version": "1.12.0",
    "Maintainer": "Nolwenn Le Meur <nlemeur@fhcrc.org>",
    "Author": "Nolwenn Le Meur and Robert Gentleman",
    "Title": "Phenotypes and cellular organizational units",
    "source.ver": "src/contrib/PCpheno_1.12.0.tar.gz",
    "Imports": [
      "AnnotationDbi",
      "Biobase",
      "Category",
      "GO.db",
      "graph",
      "graphics",
      "GSEABase",
      "KEGG.db",
      "methods",
      "ScISI",
      "stats"
    ],
    "Suggests": [
      "KEGG.db",
      "GO.db",
      "org.Sc.sgd.db"
    ],
    "Package": "PCpheno",
    "vignettes": [
      "vignettes/PCpheno/inst/doc/PCpheno.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "GraphsAndNetworks",
      "Proteomics",
      "Software"
    ],
    "Description": "Tools to integrate, annotate, and link phenotypes to cellular organizational units such as protein complexes and pathways.",
    "win.binary.ver": "bin/windows/contrib/2.12/PCpheno_1.12.0.zip"
  },
  "metahdep": {
    "Depends": [
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/metahdep_1.8.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/metahdep_1.8.0.tgz",
    "Version": "1.8.0",
    "Maintainer": "John R. Stevens <john.r.stevens@usu.edu>",
    "Author": "John R. Stevens, Gabriel Nicholas",
    "Title": "Hierarchical Dependence in Meta-Analysis",
    "source.ver": "src/contrib/metahdep_1.8.0.tar.gz",
    "Suggests": [
      "affyPLM"
    ],
    "Package": "metahdep",
    "vignettes": [
      "vignettes/metahdep/inst/doc/metahdep.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL-3",
    "biocViews": [
      "Bioinformatics",
      "DifferentialExpression",
      "Microarray",
      "Software"
    ],
    "Description": "Tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies",
    "win.binary.ver": "bin/windows/contrib/2.12/metahdep_1.8.0.zip"
  },
  "spikeLI": {
    "win64.binary.ver": "bin/windows64/contrib/2.12/spikeLI_2.10.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/spikeLI_2.10.0.tgz",
    "Version": "2.10.0",
    "Maintainer": "Enrico Carlon <enrico.carlon@fys.kuleuven.be>",
    "Author": "Delphine Baillon, Paul Leclercq <paulleclercq@hotmail.com>, Sarah Ternisien, Thomas Heim, Enrico Carlon <enrico.carlon@fys.kuleuven.be>",
    "Title": "Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool",
    "source.ver": "src/contrib/spikeLI_2.10.0.tar.gz",
    "Imports": [
      "graphics",
      "grDevices",
      "stats",
      "utils"
    ],
    "Package": "spikeLI",
    "vignettes": [
      "vignettes/spikeLI/inst/doc/collapse_A14.pdf",
      "vignettes/spikeLI/inst/doc/Ivsc.pdf",
      "vignettes/spikeLI/inst/doc/IvsDG_TagE.pdf",
      "vignettes/spikeLI/inst/doc/langmuir2.pdf",
      "vignettes/spikeLI/inst/doc/spikeLI.pdf"
    ],
    "License": "GPL",
    "biocViews": [
      "Microarray",
      "QualityControl",
      "Software"
    ],
    "Description": "SpikeLI is a package that performs the analysis of the Affymetrix spike-in data using the Langmuir Isotherm. The aim of this package is to show the advantages of a physical-chemistry based analysis of the Affymetrix microarray data compared to the traditional methods. The spike-in (or Latin square) data for the HGU95 and HGU133 chipsets have been downloaded from the Affymetrix web site. The model used in the spikeLI package is described in details in E. Carlon and T. Heim, Physica A 362, 433 (2006).",
    "win.binary.ver": "bin/windows/contrib/2.12/spikeLI_2.10.0.zip"
  },
  "rHVDM": {
    "Depends": [
      "R (>= 2.3)",
      "R2HTML (>= 1.5)",
      "affy (>= 1.23.4)",
      "minpack.lm (>= 1.0-5)",
      "Biobase (>= 2.5.5)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/rHVDM_1.16.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/rHVDM_1.16.0.tgz",
    "Version": "1.16.0",
    "Maintainer": "Martino Barenco<m.barenco@ucl.ac.uk>",
    "Author": "Martino Barenco",
    "Title": "Hidden Variable Dynamic Modeling",
    "source.ver": "src/contrib/rHVDM_1.16.0.tar.gz",
    "Package": "rHVDM",
    "vignettes": [
      "vignettes/rHVDM/inst/doc/rHVDM.pdf"
    ],
    "License": "GPL-2",
    "biocViews": [
      "Classification",
      "GraphsAndNetworks",
      "Microarray",
      "Software",
      "Transcription"
    ],
    "Description": "A R implementation of HVDM (Genome Biol 2006, V7(3) R25)",
    "win.binary.ver": "bin/windows/contrib/2.12/rHVDM_1.16.0.zip"
  },
  "GeneSelector": {
    "Depends": [
      "R (>= 2.5.1)",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/GeneSelector_2.6.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/GeneSelector_2.6.0.tgz",
    "Version": "2.6.0",
    "Maintainer": "Martin Slawski <martin.slawski@cs.uni-sb.de>",
    "Author": "Martin Slawski <ms@cs.uni-sb.de>, Anne-Laure Boulesteix <boulesteix@ibe.med.uni-muenchen.de>.",
    "Title": "Stability and Aggregation of ranked gene lists",
    "source.ver": "src/contrib/GeneSelector_2.6.0.tar.gz",
    "Imports": [
      "Biobase",
      "graphics",
      "grDevices",
      "methods",
      "stats",
      "samr"
    ],
    "Suggests": [
      "multtest",
      "siggenes",
      "samr",
      "limma"
    ],
    "Package": "GeneSelector",
    "vignettes": [
      "vignettes/GeneSelector/inst/doc/GeneSelector.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL (>= 2)",
    "biocViews": [
      "DifferentialExpression",
      "Software",
      "Statistics"
    ],
    "Description": "The term 'GeneSelector' refers to a filter selecting those genes which are consistently identified as differentially expressed using various statistical procedures. 'Selected' genes are those present at the top of the list in various ranking methods (currently 14). In addition, the stability of the findings can be taken into account in the final ranking by examining perturbed versions of the original data set, e.g. by leaving samples, swapping class labels, generating bootstrap replicates or adding noise. Given multiple ranked lists, one can use aggregation methods in order to find a synthesis.",
    "win.binary.ver": "bin/windows/contrib/2.12/GeneSelector_2.6.0.zip"
  },
  "GenomicFeatures": {
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      "GenomicRanges (>= 0.0.9)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/GenomicFeatures_1.2.3.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/GenomicFeatures_1.2.3.tgz",
    "Version": "1.2.3",
    "dependsOnMe": [
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      "GenomicFeatures.Mmusculus.UCSC.mm9"
    ],
    "Maintainer": "Biocore Team c/o BioC user list <bioconductor@stat.math.ethz.ch>",
    "Author": "M. Carlson, H. Pages, P. Aboyoun, S. Falcon, M. Morgan, D. Sarkar, M. Lawrence",
    "Title": "Tools for making and manipulating transcript centric annotations",
    "suggestsMe": [
      "Biostrings",
      "chipseq",
      "GenomicRanges",
      "ind1KG",
      "Rsamtools"
    ],
    "source.ver": "src/contrib/GenomicFeatures_1.2.3.tar.gz",
    "Imports": [
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      "DBI (>= 0.2-5)",
      "RSQLite (>= 0.8-1)",
      "IRanges",
      "GenomicRanges",
      "Biostrings (>= 2.17.6)",
      "rtracklayer (>= 1.7.11)",
      "biomaRt",
      "RCurl",
      "utils"
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    "Suggests": [
      "rtracklayer",
      "biomaRt",
      "org.Mm.eg.db",
      "GenomicFeatures.Hsapiens.UCSC.hg18",
      "Biostrings",
      "BSgenome",
      "BSgenome.Hsapiens.UCSC.hg18 (>= 1.3.14)",
      "RUnit"
    ],
    "Package": "GenomicFeatures",
    "vignettes": [
      "vignettes/GenomicFeatures/inst/doc/examples.pdf",
      "vignettes/GenomicFeatures/inst/doc/GenomicFeatures.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "Annotation",
      "Genetics",
      "HighThroughputSequencing",
      "Infrastructure",
      "Software"
    ],
    "Description": "A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.",
    "importsMe": [
      "geneLenDataBase",
      "GenomicFeatures.Hsapiens.UCSC.hg18",
      "GenomicFeatures.Mmusculus.UCSC.mm9"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/GenomicFeatures_1.2.3.zip"
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  "flowQ": {
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      "R (>= 2.4.0)",
      "outliers",
      "lattice",
      "flowViz",
      "methods",
      "mvoutlier",
      "bioDist",
      "parody",
      "RColorBrewer",
      "latticeExtra"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/flowQ_1.10.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/flowQ_1.10.0.tgz",
    "Version": "1.10.0",
    "Maintainer": "F. Hahne <florian.hahne@novartis.com>",
    "Author": "R. Gentleman, F. Hahne, J. Kettman, N. Le Meur, N. Gopalakrishnan",
    "Title": "Qualitiy control for flow cytometry",
    "source.ver": "src/contrib/flowQ_1.10.0.tar.gz",
    "Imports": [
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      "flowCore",
      "flowViz"
    ],
    "Package": "flowQ",
    "vignettes": [
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      "vignettes/flowQ/inst/doc/Extending-flowQ.pdf",
      "vignettes/flowQ/inst/doc/flowQStructure.pdf",
      "vignettes/flowQ/inst/doc/stainInfo.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "CellBasedAssays",
      "Flowcytometry",
      "Infrastructure",
      "Software"
    ],
    "Description": "Provides quality control and quality assessment tools for flow cytometry data.",
    "win.binary.ver": "bin/windows/contrib/2.12/flowQ_1.10.0.zip"
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  "GeneSpring": {
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      "Biobase (>= 1.5.0)",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/GeneSpring_2.24.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/GeneSpring_2.24.0.tgz",
    "Version": "2.24.0",
    "URL": "http://www.chem.agilent.com/scripts/generic.asp?lpage=34733",
    "Maintainer": "Thon de Boer <thon_deboer@agilent.com>",
    "Author": "Thon de Boer <thon_deboer@agilent.com>",
    "Title": "GeneSpring R Integration Functions",
    "source.ver": "src/contrib/GeneSpring_2.24.0.tar.gz",
    "Imports": [
      "Biobase",
      "methods",
      "utils"
    ],
    "Package": "GeneSpring",
    "vignettes": [
      "vignettes/GeneSpring/inst/doc/GeneSpring.pdf"
    ],
    "License": "GPL",
    "biocViews": [
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      "Software"
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    "Maintainer": "Matt Wilkerson <mwilkers@med.unc.edu>",
    "Author": "Matt Wilkerson",
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    "Maintainer": "James M. Ward <jmw86069@gmail.com>",
    "Author": "James M. Ward <jmw86069@gmail.com> with contributions from Yunling Shi, Cindy Richards, John P. Cogswell",
    "Title": "miRNApath: Pathway Enrichment for miRNA Expression Data",
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    "URL": "http://www.metnetdb.org/MetNet_exploRase.htm",
    "Maintainer": "Michael Lawrence <mflawren@fhcrc.org>",
    "Author": "Michael Lawrence, Eun-kyung Lee, Dianne Cook, Jihong Kim, Hogeun An, and Dongshin Kim",
    "Title": "GUI for exploratory data analysis of systems biology data",
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    "Maintainer": "Arnaud Droit <arnaud.droit@ircm.qc.ca>",
    "Author": "Arnaud Droit, Raphael Gottardo, Gordon Robertson and Leiping Li",
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    "Maintainer": "Jianhua Zhang <jzhang@jimmy.harvard.edu>",
    "Author": "Jianhua Zhang",
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    "Maintainer": "Biocore Team c/o BioC user list <bioconductor@stat.math.ethz.ch>",
    "Author": "Lara Lusa <lusa@ifom-firc.it>, R. Gentleman, M. Ruschhaupt",
    "Title": "MetaAnalysis for High Throughput Experiments",
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    "source.ver": "src/contrib/GeneMeta_1.22.0.tar.gz",
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    "Description": "A collection of meta-analysis tools for analysing high throughput experimental data",
    "win.binary.ver": "bin/windows/contrib/2.12/GeneMeta_1.22.0.zip"
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    "Maintainer": "Biocore Team c/o BioC user list <bioconductor@stat.math.ethz.ch>",
    "Author": "R. Gentleman, V. Carey, W. Huber, F. Hahne",
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    "Description": "Some basic functions for filtering genes",
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    "URL": "http://www.humgen.nl/MicroarrayAnalysisGroup.html",
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    "Version": "1.10.0",
    "Maintainer": "Martin Morgan <mtmorgan@fhcrc.org>",
    "Author": "Martin Morgan, Robert Gentleman",
    "Title": "Affymetrix GeneChip software compatibility",
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    "License": "Artistic-2.0",
    "biocViews": [
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      "Software"
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    "Description": "This package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to download and manage local data bases of Affynmetrix NetAffx annotation files. The package also provides access to GeneChip Operating System (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation files.",
    "win.binary.ver": "bin/windows/contrib/2.12/AffyCompatible_1.10.0.zip"
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      "Biobase (>= 1.14.1)",
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    "Maintainer": "J. Toedling <joern.toedling@curie.fr>",
    "Author": "Joern Toedling, Oleg Sklyar, Tammo Krueger, Matt Ritchie, Wolfgang Huber",
    "Title": "R Investigation of ChIP-chip Oligoarrays",
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      "vsn"
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    "Description": "The package Ringo facilitates the primary analysis of ChIP-chip data. The main functionalities of the package are data read-in, quality assessment, data visualisation and identification of genomic regions showing enrichment in ChIP-chip. The package has functions to deal with two-color oligonucleotide microarrays from NimbleGen used in ChIP-chip projects, but also contains more general functions for ChIP-chip data analysis, given that the data is supplied as RGList (raw) or ExpressionSet (pre- processed). The package employs functions from various other packages of the Bioconductor project and provides additional ChIP-chip-specific and NimbleGen-specific functionalities.",
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    "Maintainer": "Habil Zare <hzare@bccrc.ca>",
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    "Title": "Identifies cell population in flow cytometry data.",
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    "Description": "Given a matrix of coordinates as input, SamSPECTRAL first builds the communities to sample the data points. Then, it builds a graph and after weighting the edges by conductance computation, the graph is passed to a classic spectral clustering algorithm to find the spectral clusters. The last stage of SamSPECTRAL is to combine the spectral clusters. The resulting \"connected components\" estimate biological cell populations in the data sample. For instructions on manual installation, refer to the PDF file provided in the following documentation.",
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    "URL": "http://astor.som.jhmi.edu/MergeMaid",
    "Maintainer": "Xiaogang Zhong <zhong@ams.jhu.edu>",
    "Author": "Xiaogang Zhong <zhong@ams.jhu.edu> Leslie Cope <cope@jhu.edu> Elizabeth Garrett <esg@jhu.edu> Giovanni Parmigiani <gp@jhu.edu>",
    "Title": "Merge Maid",
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    "License": "GPL (>= 2)",
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    "Description": "The functions in this R extension are intended for cross-study comparison of gene expression array data. Required from the user is gene expression matrices, their corresponding gene-id vectors and other useful information, and they could be 'list','matrix', or 'ExpressionSet'. The main function is 'mergeExprs' which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function 'intcor' calculate the correlation coefficients. Other functions use the output from 'modelOutcome' to graphically display the results and cross-validate associations of gene expression data with survival.",
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    "Maintainer": "Biocore Team c/o BioC user list <bioconductor@stat.math.ethz.ch>",
    "Author": "R. Gentleman, Biocore",
    "Title": "Graphics related functions for Bioconductor",
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    "Author": "Jelle Goeman <j.j.goeman@lumc.nl> and Jan Oosting <j.oosting@lumc.nl>",
    "Title": "Testing groups of covariates/features for association with a response variable, with applications to gene set testing",
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/rbsurv_2.8.0.tgz",
    "Version": "2.8.0",
    "URL": "http://www.korea.ac.kr/~stat2242/",
    "Maintainer": "Soo-heang Eo <hanansh@korea.ac.kr>",
    "Author": "HyungJun Cho <hj4cho@korea.ac.kr>, Sukwoo Kim <s4kim@korea.ac.kr>, Soo-heang Eo <hanansh@korea.ac.kr>, Jaewoo Kang <kangj@korea.ac.kr>",
    "Title": "Robust likelihood-based survival modeling with microarray data",
    "source.ver": "src/contrib/rbsurv_2.8.0.tar.gz",
    "Package": "rbsurv",
    "vignettes": [
      "vignettes/rbsurv/inst/doc/rbsurv.pdf"
    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "Bioinformatics",
      "Microarray",
      "Software"
    ],
    "Description": "This package selects genes associated with survival.",
    "win.binary.ver": "bin/windows/contrib/2.12/rbsurv_2.8.0.zip"
  },
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      "R (>= 2.0.0)",
      "methods",
      "widgetTools (>= 1.1.7)",
      "DynDoc (>= 1.3.0)",
      "tools"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/tkWidgets_1.28.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/tkWidgets_1.28.0.tgz",
    "Version": "1.28.0",
    "dependsOnMe": [
      "cosmoGUI",
      "oneChannelGUI"
    ],
    "Maintainer": "J. Zhang <jzhang@jimmy.harvard.edu>",
    "Author": "J. Zhang <jzhang@jimmy.harvard.edu>",
    "Title": "R based tk widgets",
    "suggestsMe": [
      "affy",
      "affyQCReport",
      "annotate",
      "Biobase",
      "genefilter",
      "marray"
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    "source.ver": "src/contrib/tkWidgets_1.28.0.tar.gz",
    "Suggests": [
      "Biobase"
    ],
    "Package": "tkWidgets",
    "vignettes": [
      "vignettes/tkWidgets/inst/doc/importWizard.pdf",
      "vignettes/tkWidgets/inst/doc/tkWidgets.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "Infrastructure",
      "Software"
    ],
    "Description": "Widgets to provide user interfaces. tcltk should have been installed for the widgets to run.",
    "importsMe": [
      "Mfuzz",
      "OLINgui"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/tkWidgets_1.28.0.zip"
  },
  "flowViz": {
    "Depends": [
      "R (>= 2.7.0)",
      "flowCore (>= 1.5.17)",
      "lattice"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/flowViz_1.14.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/flowViz_1.14.0.tgz",
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    "dependsOnMe": [
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      "flowQ",
      "flowTrans",
      "plateCore"
    ],
    "Maintainer": "Florian Hahne <florian.hahne@novartis.com>",
    "Author": "B. Ellis, R. Gentleman, F. Hahne, N. Le Meur, D. Sarkar",
    "Title": "Visualization for flow cytometry",
    "suggestsMe": [
      "flowCore",
      "flowStats"
    ],
    "source.ver": "src/contrib/flowViz_1.14.0.tar.gz",
    "Imports": [
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      "flowCore",
      "graphics",
      "grDevices",
      "grid",
      "KernSmooth",
      "lattice",
      "latticeExtra",
      "MASS",
      "methods",
      "RColorBrewer",
      "stats",
      "utils"
    ],
    "Suggests": [
      "RColorBrewer",
      "IDPmisc"
    ],
    "Package": "flowViz",
    "vignettes": [
      "vignettes/flowViz/inst/doc/filters.pdf"
    ],
    "Archs": "i386, x64",
    "License": "Artistic-2.0",
    "biocViews": [
      "CellBasedAssays",
      "Flowcytometry",
      "Infrastructure",
      "Software",
      "Visualization"
    ],
    "Description": "Provides visualization tools for flow cytometry data.",
    "importsMe": [
      "flowFP",
      "flowQ",
      "flowStats",
      "flowTrans",
      "flowUtils"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/flowViz_1.14.0.zip"
  },
  "ontoCAT": {
    "Depends": [
      "rJava",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/ontoCAT_1.0.0.zip",
    "Version": "1.0.0",
    "Maintainer": "Natalja Kurbatova <natalja@ebi.ac.uk>",
    "Author": "Misha Kapushevsky, Pavel Kurnosov, Natalja Kurbatova",
    "Title": "Ontology parsing",
    "source.ver": "src/contrib/ontoCAT_1.0.0.tar.gz",
    "Package": "ontoCAT",
    "vignettes": [
      "vignettes/ontoCAT/inst/doc/ontoCAT.pdf"
    ],
    "License": "Apache License",
    "biocViews": [
      "Classification",
      "DataRepresentation",
      "Software"
    ],
    "Description": "The ontoCAT package provides a simple interface to ontology described in OWL or OBO format. Package can load the ontology from a local file or on the fly from a URL. Number of functions allow to parse an ontology, search terms in it, find out term parents and children.",
    "win.binary.ver": "bin/windows/contrib/2.12/ontoCAT_1.0.0.zip"
  },
  "les": {
    "Depends": [
      "R (>= 2.11.0)",
      "methods",
      "graphics",
      "fdrtool"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/les_1.0.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/les_1.0.0.tgz",
    "Version": "1.0.0",
    "URL": "http://www.fdmold.uni-freiburg.de/~jgehring/",
    "Maintainer": "Julian Gehring <julian.gehring@fdm.uni-freiburg.de>",
    "Author": "Julian Gehring, Clemens Kreutz, Jens Timmer",
    "Title": "Identifying Loci of Enhanced Significance in Tiling Microarray Data",
    "source.ver": "src/contrib/les_1.0.0.tar.gz",
    "Imports": [
      "boot",
      "gplots",
      "GSRI (>= 1.1.7)",
      "RColorBrewer"
    ],
    "Suggests": [
      "Biobase",
      "limma"
    ],
    "Package": "les",
    "vignettes": [
      "vignettes/les/inst/doc/les.pdf"
    ],
    "License": "GPL-3",
    "biocViews": [
      "Bioinformatics",
      "ChIPchip",
      "DNAMethylation",
      "DifferentialExpression",
      "Microarray",
      "Software",
      "Transcription"
    ],
    "Description": "The 'les' package estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip or methylation experiments. The package provides a universal framework suitable for identifying regulatory effects in tiling microarray data sets and is independent of the underlying statistics at the level of single probes.",
    "Enhances": [
      "multicore"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/les_1.0.0.zip"
  },
  "sizepower": {
    "Depends": [
      "stats"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/sizepower_1.20.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/sizepower_1.20.0.tgz",
    "Version": "1.20.0",
    "Maintainer": "Weiliang Qiu <weiliang.qiu@gmail.com>",
    "Author": "Weiliang Qiu <weiliang.qiu@gmail.com> and Mei-Ling Ting Lee <meilinglee@sph.osu.edu> and George Alex Whitmore <george.whitmore@mcgill.ca>",
    "Title": "Sample Size and Power Calculation in Micorarray Studies",
    "suggestsMe": [
      "oneChannelGUI"
    ],
    "source.ver": "src/contrib/sizepower_1.20.0.tar.gz",
    "Package": "sizepower",
    "vignettes": [
      "vignettes/sizepower/inst/doc/sizepower.pdf"
    ],
    "License": "LGPL",
    "biocViews": [
      "Bioinformatics",
      "Microarray",
      "Software"
    ],
    "Description": "This package has been prepared to assist users in computing either a sample size or power value for a microarray experimental study. The user is referred to the cited references for technical background on the methodology underpinning these calculations. This package provides support for five types of sample size and power calculations. These five types can be adapted in various ways to encompass many of the standard designs encountered in practice.",
    "win.binary.ver": "bin/windows/contrib/2.12/sizepower_1.20.0.zip"
  },
  "panp": {
    "Depends": [
      "R (>= 2.5.0)",
      "affy (>= 1.23.4)",
      "Biobase (>= 2.5.5)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/panp_1.20.1.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/panp_1.20.1.tgz",
    "Version": "1.20.1",
    "Maintainer": "Peter Warren <peter.warren@verizon.net>",
    "Author": "Peter Warren",
    "Title": "Presence-Absence Calls from Negative Strand Matching Probesets",
    "source.ver": "src/contrib/panp_1.20.1.tar.gz",
    "Imports": [
      "Biobase",
      "methods",
      "stats",
      "utils"
    ],
    "Package": "panp",
    "vignettes": [
      "vignettes/panp/inst/doc/panp.pdf"
    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "Software"
    ],
    "Description": "A function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date.",
    "win.binary.ver": "bin/windows/contrib/2.12/panp_1.20.1.zip"
  },
  "bgafun": {
    "Depends": [
      "made4",
      "seqinr",
      "ade4"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/bgafun_1.12.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/bgafun_1.12.0.tgz",
    "Version": "1.12.0",
    "Maintainer": "Iain Wallace <iain.wallace@ucd.ie>",
    "Author": "Iain Wallace",
    "Title": "BGAfun A method to identify specifity determining residues in protein families",
    "source.ver": "src/contrib/bgafun_1.12.0.tar.gz",
    "Package": "bgafun",
    "vignettes": [
      "vignettes/bgafun/inst/doc/bgafun.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "Bioinformatics",
      "Classification",
      "Software"
    ],
    "Description": "A method to identify specifity determining residues in protein families using Between Group Analysis",
    "win.binary.ver": "bin/windows/contrib/2.12/bgafun_1.12.0.zip"
  },
  "LBE": {
    "Depends": [
      "stats"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/LBE_1.18.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/LBE_1.18.0.tgz",
    "Version": "1.18.0",
    "Maintainer": "Cyril Dalmasso <dalmasso@vjf.inserm.fr>",
    "Author": "Cyril Dalmasso",
    "Title": "Estimation of the false discovery rate.",
    "source.ver": "src/contrib/LBE_1.18.0.tar.gz",
    "Imports": [
      "graphics",
      "grDevices",
      "methods",
      "stats",
      "utils"
    ],
    "Suggests": [
      "qvalue"
    ],
    "Package": "LBE",
    "vignettes": [
      "vignettes/LBE/inst/doc/LBE.pdf"
    ],
    "License": "GPL-2",
    "biocViews": [
      "Bioinformatics",
      "MultipleComparisons",
      "Software"
    ],
    "Description": "LBE is an efficient procedure for estimating the proportion of true null hypotheses, the false discovery rate (and so the q-values) in the framework of estimating procedures based on the marginal distribution of the p-values without assumption for the alternative hypothesis.",
    "win.binary.ver": "bin/windows/contrib/2.12/LBE_1.18.0.zip"
  },
  "rsbml": {
    "Depends": [
      "R (>= 2.6.0)",
      "methods",
      "utils"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/rsbml_2.8.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/rsbml_2.8.0.tgz",
    "Version": "2.8.0",
    "URL": "http://www.sbml.org",
    "Maintainer": "Michael Lawrence <michafla@gene.com>",
    "Author": "Michael Lawrence <michafla@gene.com>",
    "Title": "R support for SBML, using libsbml",
    "source.ver": "src/contrib/rsbml_2.8.0.tar.gz",
    "Imports": [
      "graph",
      "utils"
    ],
    "Package": "rsbml",
    "vignettes": [
      "vignettes/rsbml/inst/doc/quick-start.pdf"
    ],
    "Archs": "i386",
    "License": "Artistic-2.0",
    "biocViews": [
      "GraphsAndNetworks",
      "Software"
    ],
    "Description": "Links R to libsbml for SBML parsing, validating output, provides an S4 SBML DOM, converts SBML to R graph objects. Optionally links to the SBML ODE Solver Library (SOSLib) for simulating models.",
    "SystemRequirements": "libsbml (>=3.0.3)",
    "win.binary.ver": "bin/windows/contrib/2.12/rsbml_2.8.0.zip"
  },
  "GEOsubmission": {
    "win64.binary.ver": "bin/windows64/contrib/2.12/GEOsubmission_1.2.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/GEOsubmission_1.2.0.tgz",
    "Version": "1.2.0",
    "Maintainer": "Alexandre Kuhn <kuhnam@mail.nih.gov>",
    "Author": "Alexandre Kuhn <kuhnam@mail.nih.gov>",
    "Title": "Prepares microarray data for submission to GEO",
    "source.ver": "src/contrib/GEOsubmission_1.2.0.tar.gz",
    "Imports": [
      "affy",
      "Biobase",
      "utils"
    ],
    "Package": "GEOsubmission",
    "vignettes": [
      "vignettes/GEOsubmission/inst/doc/GEOsubmission.pdf"
    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "Microarray",
      "Software"
    ],
    "Description": "Helps to easily submit a microarray dataset and the associated sample information to GEO by preparing a single file for upload (direct deposit).",
    "win.binary.ver": "bin/windows/contrib/2.12/GEOsubmission_1.2.0.zip"
  },
  "charm": {
    "Depends": [
      "R (>= 2.11.0)",
      "Biobase",
      "SQN",
      "fields",
      "RColorBrewer",
      "genefilter"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/charm_1.2.1.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/charm_1.2.1.tgz",
    "Version": "1.2.1",
    "dependsOnMe": [
      "charmData"
    ],
    "Maintainer": "Martin Aryee <aryee@jhu.edu>",
    "Author": "Martin Aryee, Peter Murakami, Harris Jaffee, Srinivasan Yegnasubramanian, Rafael Irizarry",
    "Title": "Analysis of DNA methylation data from CHARM microarrays",
    "source.ver": "src/contrib/charm_1.2.1.tar.gz",
    "Imports": [
      "BSgenome",
      "Biobase",
      "oligo (>= 1.11.31)",
      "oligoClasses(>= 1.9.42)",
      "ff",
      "preprocessCore",
      "methods",
      "stats",
      "Biostrings",
      "IRanges",
      "siggenes",
      "nor1mix",
      "gtools",
      "grDevices",
      "graphics",
      "utils"
    ],
    "Suggests": [
      "charmData",
      "BSgenome.Hsapiens.UCSC.hg18"
    ],
    "Package": "charm",
    "vignettes": [
      "vignettes/charm/inst/doc/charm.pdf"
    ],
    "License": "LGPL (>= 2)",
    "biocViews": [
      "Bioinformatics",
      "DNAMethylation",
      "Microarray",
      "Software"
    ],
    "Description": "This package implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol. It finds differentially methylated regions between samples, calculates percentage methylation estimates and includes array quality assessment tools.",
    "win.binary.ver": "bin/windows/contrib/2.12/charm_1.2.1.zip"
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  "RCytoscape": {
    "Depends": [
      "R (>= 2.11.0)",
      "graph (>= 1.26.0)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/RCytoscape_1.0.1.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/RCytoscape_1.0.1.tgz",
    "Version": "1.0.1",
    "URL": "http://db.systemsbiology.net:8080/cytoscape/RCytoscape/",
    "Maintainer": "Paul Shannon <pshannon@systemsbiology.org>",
    "Author": "Paul Shannon",
    "Title": "Display and manipulate graphs in Cytoscape",
    "source.ver": "src/contrib/RCytoscape_1.0.1.tar.gz",
    "Imports": [
      "methods",
      "XMLRPC"
    ],
    "Suggests": [
      "RUnit"
    ],
    "Package": "RCytoscape",
    "vignettes": [
      "vignettes/RCytoscape/inst/doc/RCytoscape.pdf"
    ],
    "License": "GPL",
    "biocViews": [
      "GraphsAndNetworks",
      "Software"
    ],
    "Description": "Interactvive viewing and exploration of graphs, connecting R to Cytoscape.",
    "win.binary.ver": "bin/windows/contrib/2.12/RCytoscape_1.0.1.zip"
  },
  "clusterStab": {
    "Depends": [
      "Biobase (>= 1.4.22)",
      "R (>= 1.9.0)",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/clusterStab_1.22.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/clusterStab_1.22.0.tgz",
    "Version": "1.22.0",
    "Maintainer": "James W. MacDonald <jmacdon@med.umich.edu>",
    "Author": "James W. MacDonald, Debashis Ghosh, Mark Smolkin",
    "Title": "Compute cluster stability scores for microarray data",
    "source.ver": "src/contrib/clusterStab_1.22.0.tar.gz",
    "Suggests": [
      "fibroEset",
      "genefilter"
    ],
    "Package": "clusterStab",
    "vignettes": [
      "vignettes/clusterStab/inst/doc/clusterStab.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "Clustering",
      "Software"
    ],
    "Description": "This package can be used to estimate the number of clusters in a set of microarray data, as well as test the stability of these clusters.",
    "win.binary.ver": "bin/windows/contrib/2.12/clusterStab_1.22.0.zip"
  },
  "PLPE": {
    "Depends": [
      "R (>= 2.6.2)",
      "Biobase (>= 2.5.5)",
      "LPE",
      "MASS",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/PLPE_1.10.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/PLPE_1.10.0.tgz",
    "Version": "1.10.0",
    "URL": "http://www.korea.ac.kr/~stat2242/",
    "Maintainer": "Soo-heang Eo <hanansh@korea.ac.kr>",
    "Author": "HyungJun Cho <hj4cho@korea.ac.kr> and Jae K. Lee <jaeklee@virginia.edu>",
    "Title": "Local Pooled Error Test for Differential Expression with Paired High-throughput Data",
    "source.ver": "src/contrib/PLPE_1.10.0.tar.gz",
    "Package": "PLPE",
    "vignettes": [
      "vignettes/PLPE/inst/doc/PLPE.pdf"
    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "DifferentialExpression",
      "Microarray",
      "Proteomics",
      "Software"
    ],
    "Description": "This package performs tests for paired high-throughput data.",
    "win.binary.ver": "bin/windows/contrib/2.12/PLPE_1.10.0.zip"
  },
  "BioSeqClass": {
    "win64.binary.ver": "bin/windows64/contrib/2.12/BioSeqClass_1.8.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/BioSeqClass_1.8.0.tgz",
    "Version": "1.8.0",
    "Maintainer": "Li Hong <sysptm@gmail.com>",
    "Author": "Li Hong sysptm@gmail.com",
    "Title": "Classification for Biological Sequences",
    "source.ver": "src/contrib/BioSeqClass_1.8.0.tar.gz",
    "Imports": [
      "Biostrings",
      "ipred",
      "e1071",
      "klaR",
      "randomForest",
      "class",
      "tree",
      "nnet",
      "rpart",
      "party",
      "foreign",
      "Biobase",
      "utils",
      "stats",
      "grDevices"
    ],
    "Package": "BioSeqClass",
    "vignettes": [
      "vignettes/BioSeqClass/inst/doc/BioSeqClass.pdf",
      "vignettes/BioSeqClass/inst/doc/cvFFSClassify0005.pdf",
      "vignettes/BioSeqClass/inst/doc/FeatureSets16.pdf",
      "vignettes/BioSeqClass/inst/doc/workflow.pdf"
    ],
    "License": "LGPL (>= 2.0)",
    "biocViews": [
      "Classification",
      "Software"
    ],
    "Description": "Extracting Features from Biological Sequences and Building Classification Model",
    "win.binary.ver": "bin/windows/contrib/2.12/BioSeqClass_1.8.0.zip"
  },
  "RDRToolbox": {
    "Depends": [
      "R (>= 2.9.0)",
      "rgl"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/RDRToolbox_1.0.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/RDRToolbox_1.0.0.tgz",
    "Version": "1.0.0",
    "Maintainer": "Christoph Bartenhagen <christoph.bartenhagen@ukmuenster.de>",
    "Author": "Christoph Bartenhagen",
    "Title": "A package for nonlinear dimension reduction with Isomap and LLE.",
    "source.ver": "src/contrib/RDRToolbox_1.0.0.tar.gz",
    "Imports": [
      "graphics",
      "grDevices",
      "methods",
      "stats",
      "MASS",
      "rgl"
    ],
    "Suggests": [
      "golubEsets"
    ],
    "Package": "RDRToolbox",
    "vignettes": [
      "vignettes/RDRToolbox/inst/doc/plot3D.pdf",
      "vignettes/RDRToolbox/inst/doc/RDRToolbox-003.pdf",
      "vignettes/RDRToolbox/inst/doc/SwissRoll.pdf",
      "vignettes/RDRToolbox/inst/doc/vignette.pdf"
    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "ClusterValidation",
      "Dimension",
      "DimensionReduction",
      "FeatureExtraction",
      "Microarray",
      "Software",
      "Visualization"
    ],
    "Description": "A package for nonlinear dimension reduction using the Isomap and LLE algorithm. It also includes a routine for computing the Davis-Bouldin-Index for cluster validation, a plotting tool and a data generator for microarray gene expression data and for the Swiss Roll dataset.",
    "win.binary.ver": "bin/windows/contrib/2.12/RDRToolbox_1.0.0.zip"
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    "Depends": [
      "affyPLM",
      "vsn"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/arrayQualityMetrics_3.2.4.zip",
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    "Version": "3.2.4",
    "Maintainer": "Audrey Kauffmann <kauffmann@bergonie.org>",
    "Author": "Audrey Kauffmann, Wolfgang Huber",
    "Title": "Quality metrics on microarray data sets",
    "suggestsMe": [
      "ArrayExpress"
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    "Imports": [
      "Biobase",
      "RColorBrewer",
      "affy",
      "beadarray",
      "genefilter",
      "grDevices",
      "graphics",
      "hwriter",
      "lattice",
      "latticeExtra",
      "limma",
      "marray",
      "methods",
      "RJSONIO",
      "simpleaffy",
      "stats",
      "stats4",
      "SVGAnnotation (>= 0.7.2)",
      "utils",
      "XML"
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    "Suggests": [
      "ALLMLL",
      "CCl4"
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    "Package": "arrayQualityMetrics",
    "vignettes": [
      "vignettes/arrayQualityMetrics/inst/doc/aqm.pdf",
      "vignettes/arrayQualityMetrics/inst/doc/arrayQualityMetrics.pdf"
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    "License": "LGPL (>= 2)",
    "biocViews": [
      "Microarray",
      "OneChannel",
      "QualityControl",
      "ReportWriting",
      "Software",
      "TwoChannel"
    ],
    "Description": "This package generates a quality metrics report on ExpressionSet, NChannelSet, AffyBatch or BeadLevelList objects containing microarray data with one or two channels.",
    "win.binary.ver": "bin/windows/contrib/2.12/arrayQualityMetrics_3.2.4.zip"
  },
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      "R (>= 2.7.0)",
      "methods",
      "Biobase (>= 2.9.0)",
      "snpMatrix(>= 1.7.6)",
      "RSQLite"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/GGBase_3.10.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/GGBase_3.10.0.tgz",
    "Version": "3.10.0",
    "dependsOnMe": [
      "ceu1kg",
      "ceuhm3",
      "encoDnaseI",
      "GGdata",
      "GGtools"
    ],
    "Maintainer": "Vince Carey <stvjc@channing.harvard.edu>",
    "Author": "Vince Carey <stvjc@channing.harvard.edu>",
    "Title": "infrastructure for genetics of gene expression (c) 2008 VJ Carey",
    "suggestsMe": [
      "ind1KG"
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    "source.ver": "src/contrib/GGBase_3.10.0.tar.gz",
    "Imports": [
      "AnnotationDbi",
      "GSEABase"
    ],
    "Suggests": [
      "illuminaHumanv1.db",
      "SNPlocs.Hsapiens.dbSNP.20071016",
      "SNPlocs.Hsapiens.dbSNP.20090506"
    ],
    "Package": "GGBase",
    "vignettes": [
      "vignettes/GGBase/inst/doc/GGBase.pdf",
      "vignettes/GGBase/inst/doc/makeSMLset.pdf",
      "vignettes/GGBase/inst/doc/newSNPloc.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "Bioinformatics",
      "GeneticVariability",
      "Genetics",
      "SNP",
      "Software"
    ],
    "Description": "infrastructure for dealing with hapmap SNP reports, GWAS, etc.",
    "win.binary.ver": "bin/windows/contrib/2.12/GGBase_3.10.0.zip"
  },
  "MANOR": {
    "Depends": [
      "R (>= 1.8.0)",
      "GLAD"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/MANOR_1.22.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/MANOR_1.22.0.tgz",
    "Version": "1.22.0",
    "URL": "http://bioinfo.curie.fr/projects/manor/index.html",
    "Maintainer": "Pierre Neuvial <pierre.neuvial@gmail.com>",
    "Author": "Pierre Neuvial <pierre.neuvial@gmail.com>, Philippe Hupe <philippe.hupe@curie.fr>",
    "Title": "CGH Micro-Array NORmalization",
    "source.ver": "src/contrib/MANOR_1.22.0.tar.gz",
    "Imports": [
      "GLAD",
      "graphics",
      "grDevices",
      "stats",
      "utils"
    ],
    "Package": "MANOR",
    "vignettes": [
      "vignettes/MANOR/inst/doc/MANOR.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL",
    "biocViews": [
      "CopyNumberVariants",
      "DataImport",
      "Microarray",
      "Preprocessing",
      "QualityControl",
      "Software",
      "TwoChannel"
    ],
    "Description": "Importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH experiments.",
    "win.binary.ver": "bin/windows/contrib/2.12/MANOR_1.22.0.zip"
  },
  "genomes": {
    "Depends": [
      "lattice"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/genomes_1.6.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/genomes_1.6.0.tgz",
    "Version": "1.6.0",
    "Maintainer": "Chris Stubben <stubben@lanl.gov>",
    "Author": "Chris Stubben",
    "Title": "Genome sequencing project metadata",
    "source.ver": "src/contrib/genomes_1.6.0.tar.gz",
    "Imports": [
      "XML"
    ],
    "Package": "genomes",
    "vignettes": [
      "vignettes/genomes/inst/doc/genome-tables.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "Annotation",
      "Genetics",
      "Software"
    ],
    "Description": "Collects genome sequencing project metadata from NCBI and GOLD and provides tools to track, sort, group, summarize and plot the data.",
    "win.binary.ver": "bin/windows/contrib/2.12/genomes_1.6.0.zip"
  },
  "preprocessCore": {
    "Depends": [
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/preprocessCore_1.12.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/preprocessCore_1.12.0.tgz",
    "Version": "1.12.0",
    "dependsOnMe": [
      "affyPLM",
      "AgiMicroRna",
      "oneChannelGUI",
      "RefPlus"
    ],
    "Maintainer": "Benjamin Milo Bolstad <bmb@bmbolstad.com>",
    "Author": "Benjamin Milo Bolstad <bmb@bmbolstad.com>",
    "Title": "A collection of pre-processing functions",
    "source.ver": "src/contrib/preprocessCore_1.12.0.tar.gz",
    "Imports": [
      "stats"
    ],
    "Package": "preprocessCore",
    "Archs": "i386, x64",
    "License": "LGPL (>= 2)",
    "biocViews": [
      "Infrastructure",
      "Software"
    ],
    "Description": "A library of core preprocessing routines",
    "importsMe": [
      "affy",
      "charm",
      "crlmm",
      "frma",
      "frmaTools",
      "lumi",
      "MBCB",
      "oligo"
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    "win.binary.ver": "bin/windows/contrib/2.12/preprocessCore_1.12.0.zip"
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  "ChIPseqR": {
    "Depends": [
      "R (>= 2.10.0)",
      "ShortRead",
      "methods"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/ChIPseqR_1.4.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/ChIPseqR_1.4.0.tgz",
    "Version": "1.4.0",
    "Maintainer": "Peter Humburg <peter.humburg@well.ox.ac.uk>",
    "Author": "Peter Humburg",
    "Title": "Identifying Protein Binding Sites in High-Throughput Sequencing Data",
    "source.ver": "src/contrib/ChIPseqR_1.4.0.tar.gz",
    "Imports": [
      "Biostrings",
      "fBasics",
      "GenomicRanges",
      "graphics",
      "grDevices",
      "HilbertVis",
      "IRanges",
      "methods",
      "ShortRead",
      "stats",
      "timsac",
      "utils"
    ],
    "Package": "ChIPseqR",
    "vignettes": [
      "vignettes/ChIPseqR/inst/doc/Introduction.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL (>= 2)",
    "biocViews": [
      "Bioinformatics",
      "ChIPseq",
      "Infrastructure",
      "Software"
    ],
    "Description": "ChIPseqR identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. The model used to describe binding events was developed to locate nucleosomes but should flexible enough to handle other types of experiments as well.",
    "win.binary.ver": "bin/windows/contrib/2.12/ChIPseqR_1.4.0.zip"
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  "TargetSearch": {
    "Depends": [
      "R (>= 2.7.0)",
      "xcms",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/TargetSearch_1.6.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/TargetSearch_1.6.0.tgz",
    "Version": "1.6.0",
    "dependsOnMe": [
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    "Maintainer": "Alvaro Cuadros-Inostroza <inostroza@mpimp-golm.mpg.de>",
    "Author": "Alvaro Cuadros-Inostroza <inostroza@mpimp-golm.mpg.de>, Jan Lisec <lisec@mpimp-golm.mpg.de>, Henning Redestig <henning.red@googlemail.com>, Matt Hannah <matthew.hannah@bayercropscience.com>",
    "Title": "A package for the analysis of GC-MS metabolite profiling data.",
    "source.ver": "src/contrib/TargetSearch_1.6.0.tar.gz",
    "Imports": [
      "graphics",
      "grDevices",
      "methods",
      "stats",
      "tcltk",
      "utils"
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    "Suggests": [
      "TargetSearchData"
    ],
    "Package": "TargetSearch",
    "vignettes": [
      "vignettes/TargetSearch/inst/doc/TargetSearch.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL (>= 2)",
    "biocViews": [
      "MassSpectrometry",
      "Preprocessing",
      "Software",
      "Technology"
    ],
    "Description": "This packages provides a targeted pre-processing method for GC-MS data.",
    "win.binary.ver": "bin/windows/contrib/2.12/TargetSearch_1.6.0.zip"
  },
  "DEGseq": {
    "Depends": [
      "R (>= 2.8.0)",
      "qvalue",
      "ShortRead",
      "samr",
      "methods"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/DEGseq_1.4.3.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/DEGseq_1.4.3.tgz",
    "Version": "1.4.3",
    "Maintainer": "Likun Wang <wanglikun@tsinghua.edu.cn>",
    "Author": "Likun Wang <wanglikun@tsinghua.edu.cn> and Xi Wang <wang-xi05@mails.tsinghua.edu.cn>.",
    "Title": "Identify Differentially Expressed Genes from RNA-seq data",
    "source.ver": "src/contrib/DEGseq_1.4.3.tar.gz",
    "Imports": [
      "graphics",
      "grDevices",
      "methods",
      "stats",
      "utils"
    ],
    "Package": "DEGseq",
    "vignettes": [
      "vignettes/DEGseq/inst/doc/DEGseq.pdf"
    ],
    "Archs": "i386, x64",
    "License": "LGPL (>=2)",
    "biocViews": [
      "DifferentialExpression",
      "GeneExpression",
      "Preprocessing",
      "RNAseq",
      "Software"
    ],
    "Description": "DEGseq is an R package to identify differentially expressed genes from RNA-Seq data.",
    "win.binary.ver": "bin/windows/contrib/2.12/DEGseq_1.4.3.zip"
  },
  "macat": {
    "Depends": [
      "Biobase",
      "annotate"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/macat_1.24.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/macat_1.24.0.tgz",
    "Version": "1.24.0",
    "Maintainer": "Joern Toedling <joern.toedling@curie.fr>",
    "Author": "Benjamin Georgi, Matthias Heinig, Stefan Roepcke, Sebastian Schmeier, Joern Toedling",
    "Title": "MicroArray Chromosome Analysis Tool",
    "source.ver": "src/contrib/macat_1.24.0.tar.gz",
    "Suggests": [
      "hgu95av2.db",
      "stjudem"
    ],
    "Package": "macat",
    "vignettes": [
      "vignettes/macat/inst/doc/chrom6T.pdf",
      "vignettes/macat/inst/doc/chrom6TkNN.pdf",
      "vignettes/macat/inst/doc/evalkNN6.pdf",
      "vignettes/macat/inst/doc/macat.pdf",
      "vignettes/macat/inst/doc/Slidingchrom6s3.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "DifferentialExpression",
      "Microarray",
      "Software",
      "Visualization"
    ],
    "Description": "This library contains functions to investigate links between differential gene expression and the chromosomal localization of the genes. MACAT is motivated by the common observation of phenomena involving large chromosomal regions in tumor cells. MACAT is the implementation of a statistical approach for identifying significantly differentially expressed chromosome regions. The functions have been tested on a publicly available data set about acute lymphoblastic leukemia (Yeoh et al.Cancer Cell 2002), which is provided in the library 'stjudem'.",
    "win.binary.ver": "bin/windows/contrib/2.12/macat_1.24.0.zip"
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  "GeneSelectMMD": {
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      "R (>= 2.8.0)",
      "Biobase"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/GeneSelectMMD_1.6.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/GeneSelectMMD_1.6.0.tgz",
    "Version": "1.6.0",
    "Maintainer": "Weiliang Qiu <stwxq@channing.harvard.edu>",
    "Author": "Weiliang Qiu <stwxq@channing.harvard.edu>, Wenqing He <whe@stats.uwo.ca>, Xiaogang Wang <stevenw@mathstat.yorku.ca>, Ross Lazarus <ross.lazarus@channing.harvard.edu>.",
    "Title": "Gene selection based on the marginal distributions of gene profiles that characterized by a mixture of three-component multivariate distributions",
    "source.ver": "src/contrib/GeneSelectMMD_1.6.0.tar.gz",
    "Imports": [
      "Biobase",
      "MASS",
      "graphics",
      "stats",
      "survival"
    ],
    "Suggests": [
      "ALL"
    ],
    "Package": "GeneSelectMMD",
    "vignettes": [
      "vignettes/GeneSelectMMD/inst/doc/gsMMD.pdf"
    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "Bioinformatics",
      "DifferentialExpression",
      "Software"
    ],
    "Description": "Gene selection based on a mixture of marginal distributions",
    "win.binary.ver": "bin/windows/contrib/2.12/GeneSelectMMD_1.6.0.zip"
  },
  "sagenhaft": {
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      "R (>= 2.5)",
      "SparseM (>= 0.73)",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/sagenhaft_1.20.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/sagenhaft_1.20.0.tgz",
    "Version": "1.20.0",
    "URL": "http://tagcalling.mbgproject.org",
    "Maintainer": "Tim Beissbarth <beissbarth@wehi.edu.au>",
    "Author": "Tim Beissbarth <beissbarth@wehi.edu.au>, with contributions from Gordon Smyth <smyth@wehi.edu.au> and Lavinia Hyde <hyde@wehi.edu.au>.",
    "Title": "Collection of functions for reading and comparing SAGE libraries",
    "source.ver": "src/contrib/sagenhaft_1.20.0.tar.gz",
    "Imports": [
      "graphics",
      "methods",
      "SparseM",
      "stats",
      "utils"
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    "Package": "sagenhaft",
    "vignettes": [
      "vignettes/sagenhaft/inst/doc/SAGEnhaft.pdf"
    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "SAGE",
      "Software"
    ],
    "Description": "This package implements several functions useful for analysis of SAGE (Serial Analysis of Gene Expressen) data, i.e. extraction of a SAGE library from sequence files, sequence error correction, library comparison.",
    "win.binary.ver": "bin/windows/contrib/2.12/sagenhaft_1.20.0.zip"
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  "HTqPCR": {
    "Depends": [
      "Biobase",
      "RColorBrewer",
      "limma"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/HTqPCR_1.4.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/HTqPCR_1.4.0.tgz",
    "Version": "1.4.0",
    "URL": "http://www.ebi.ac.uk/bertone/software",
    "Maintainer": "Heidi Dvinge <heidi@ebi.ac.uk>",
    "Author": "Heidi Dvinge, Paul Bertone",
    "Title": "Automated analysis of high-throughput qPCR data",
    "source.ver": "src/contrib/HTqPCR_1.4.0.tar.gz",
    "Imports": [
      "affy",
      "Biobase",
      "gplots",
      "graphics",
      "grDevices",
      "limma",
      "methods",
      "RColorBrewer",
      "stats",
      "utils"
    ],
    "Suggests": [
      "statmod"
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    "Package": "HTqPCR",
    "vignettes": [
      "vignettes/HTqPCR/inst/doc/HTqPCR.pdf"
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    "License": "Artistic-2.0",
    "biocViews": [
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      "DataImport",
      "DifferentialExpression",
      "GeneExpression",
      "MicrotitrePlateAssay",
      "MultipleComparisons",
      "Preprocessing",
      "QualityControl",
      "Software",
      "Visualization"
    ],
    "Description": "Analysis of Ct values from quantitative real-time PCR (qPCR) assays. Data can be analyzed in high throughput across multiple conditions or replicates, and in spatially-defined formats such ABI TaqMan Low Density Arrays and conventional 96- or 384-well plates. HTqPCR handles data loading, quality assessment, normalization, visualization and parametric or non-parametric testing for statistical significance in Ct values between features (e.g. genes, microRNAs).",
    "win.binary.ver": "bin/windows/contrib/2.12/HTqPCR_1.4.0.zip"
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  "hyperdraw": {
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      "methods",
      "grid",
      "graph",
      "hypergraph",
      "Rgraphviz"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/hyperdraw_1.2.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/hyperdraw_1.2.0.tgz",
    "Version": "1.2.0",
    "Maintainer": "Paul Murrell <p.murrell@auckland.ac.nz>",
    "Author": "Paul Murrell",
    "Title": "Visualizing Hypergaphs",
    "source.ver": "src/contrib/hyperdraw_1.2.0.tar.gz",
    "Package": "hyperdraw",
    "vignettes": [
      "vignettes/hyperdraw/inst/doc/hyperdraw.pdf"
    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "GraphsAndNetworks",
      "Software"
    ],
    "Description": "Functions for visualizing hypergraphs.",
    "SystemRequirements": "graphviz",
    "win.binary.ver": "bin/windows/contrib/2.12/hyperdraw_1.2.0.zip"
  },
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      "R (>= 2.10.0)",
      "fdrtool"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/GSRI_1.2.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/GSRI_1.2.0.tgz",
    "Version": "1.2.0",
    "URL": "http://www.fdmold.uni-freiburg.de/~jgehring/",
    "Maintainer": "Julian Gehring <julian.gehring@fdm.uni-freiburg.de>",
    "Author": "Kilian Bartholome, Julian Gehring, Clemens Kreutz, Jens Timmer",
    "Title": "Gene Set Regulation Index",
    "source.ver": "src/contrib/GSRI_1.2.0.tar.gz",
    "Imports": [
      "boot",
      "graphics",
      "stats",
      "utils",
      "genefilter"
    ],
    "Package": "GSRI",
    "vignettes": [
      "vignettes/GSRI/inst/doc/gsri.pdf"
    ],
    "License": "GPL-3",
    "biocViews": [
      "DifferentialExpression",
      "Genetics",
      "Microarray",
      "Software",
      "Transcription"
    ],
    "Description": "Estimates the number of differentially expressed genes in a gene set with the Gene Set Regulation Index (GSRI).",
    "importsMe": [
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    "win.binary.ver": "bin/windows/contrib/2.12/GSRI_1.2.0.zip"
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      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/BufferedMatrix_1.14.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/BufferedMatrix_1.14.0.tgz",
    "Version": "1.14.0",
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    "Maintainer": "Benjamin Milo Bolstad <bmb@bmbolstad.com>",
    "Author": "Benjamin Milo Bolstad <bmb@bmbolstad.com>",
    "Title": "A matrix data storage object held in temporary files",
    "source.ver": "src/contrib/BufferedMatrix_1.14.0.tar.gz",
    "Package": "BufferedMatrix",
    "vignettes": [
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      "vignettes/BufferedMatrix/inst/doc/BufferedMatrixPicture1.pdf",
      "vignettes/BufferedMatrix/inst/doc/BufferedMatrixPicture2.pdf",
      "vignettes/BufferedMatrix/inst/doc/BufferedMatrixPicture3.pdf",
      "vignettes/BufferedMatrix/inst/doc/BufferedMatrixPicture4.pdf",
      "vignettes/BufferedMatrix/inst/doc/BufferedMatrixPicture5.pdf"
    ],
    "Archs": "i386, x64",
    "License": "LGPL (>= 2)",
    "biocViews": [
      "Infrastructure",
      "Software"
    ],
    "Description": "A tabular style data object where most data is stored outside main memory. A buffer is used to speed up access to data.",
    "win.binary.ver": "bin/windows/contrib/2.12/BufferedMatrix_1.14.0.zip"
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      "methods",
      "utils",
      "seqLogo"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/cosmo_1.16.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/cosmo_1.16.0.tgz",
    "Version": "1.16.0",
    "dependsOnMe": [
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    "URL": "http://cosmoweb.berkeley.edu/intro.html, http://www.bepress.com/sagmb/vol6/iss1/art8",
    "Maintainer": "Oliver Bembom <oliver.bembom@gmail.com>",
    "Author": "Oliver Bembom, Fabian Gallusser, and Sandrine Dudoit",
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    "Author": "Adam Ameur <Adam.Ameur@genpat.uu.se>",
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    "Description": "Functions and classes for de novo prediction of transcription factor binding consensus by heuristic search",
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    "Author": "Tim Yates <tyates@picr.man.ac.uk>",
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    "Author": "VJ Carey <stvjc@channing.harvard.edu>, BJ Harshfield <rebjh@channing.harvard.edu>, S Falcon <sfalcon@fhcrc.org>",
    "Title": "Categorized views of R package repositories",
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    "Description": "structures for vocabularies and narratives of views",
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    "Title": "Parametric Gene Set Enrichment Analysis",
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    "Maintainer": "Xuejun Arthur Li <xueli@coh.org>",
    "Author": "Xiwei Wu <xwu@coh.org>, Xuejun Arthur Li <xueli@coh.org>",
    "Title": "Affymetrix Quality Assessment and Analysis Tool",
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      "estrogen",
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    "Author": "Kyle A. Furge <kyle.furge@vai.org> and Karl Dykema <karl.dykema@vai.org>",
    "Title": "Regional Expression Biases",
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    "biocViews": [
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      "Software",
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      "graphics"
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    "URL": "http://bioinformatics.oxfordjournals.org/cgi/reprint/btn577v1",
    "Maintainer": "Adi Laurentiu Tarca <atarca@med.wayne.edu>",
    "Author": "Adi Laurentiu Tarca <atarca@med.wayne.edu>, Purvesh Kathri <purvesh@cs.wayne.edu> and Sorin Draghici <sorin@wayne.edu>",
    "Title": "Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations",
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      "Rgraphviz",
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    "vignettes": [
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    "License": "GPL (>= 2)",
    "biocViews": [
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      "Microarray",
      "Software"
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    "Description": "This package implements the Signaling Pathway Impact Analysis (SPIA) which uses the information form a list of differentially expressed genes and their log fold changes together with signaling pathways topology, in order to identify the pathways most relevant to the condition under the study.",
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    "URL": "http://www.thp.uni-koeln.de/~berg/GraphAlignment/",
    "Maintainer": "Joern P. Meier <mail@ionflux.org>",
    "Author": "Joern P. Meier <mail@ionflux.org>, Michal Kolar, Ville Mustonen, Michael Laessig, and Johannes Berg.",
    "Title": "GraphAlignment",
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    "Package": "GraphAlignment",
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      "vignettes/GraphAlignment/inst/doc/align_principle_short1.pdf",
      "vignettes/GraphAlignment/inst/doc/align_principle2b1.pdf",
      "vignettes/GraphAlignment/inst/doc/align_principle2c1.pdf",
      "vignettes/GraphAlignment/inst/doc/binning-01a.pdf",
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    "Archs": "i386, x64",
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    "Description": "Graph alignment is an extension package for the R programming environment which provides functions for finding an alignment between two networks based on link and node similarity scores. (J. Berg and M. Laessig, \"Cross-species analysis of biological networks by Bayesian alignment\", PNAS 103 (29), 10967-10972 (2006))",
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      "xtable"
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    "Maintainer": "Gregory R. Warnes <greg@random-technologies-llc.com>",
    "Author": "Gregory R. Warnes, Peng Liu, and Fasheng Li",
    "Title": "Estimate Microarray Sample Size",
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    "biocViews": [
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      "DifferentialExpression",
      "Microarray",
      "Software"
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    "Description": "Functions for computing and displaying sample size information for gene expression arrays.",
    "win.binary.ver": "bin/windows/contrib/2.12/ssize_1.24.0.zip"
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      "affy",
      "affxparser"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/Starr_1.6.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/Starr_1.6.0.tgz",
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    "Maintainer": "Benedikt Zacher <zacher@lmb.uni-muenchen.de>",
    "Author": "Benedikt Zacher, Johannes Soeding, Pei Fen Kuan, Matthias Siebert, Achim Tresch",
    "Title": "Simple tiling array analysis of Affymetrix ChIP-chip data",
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    "Imports": [
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      "MASS"
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    "Package": "Starr",
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    "Archs": "i386, x64",
    "License": "Artistic-2.0",
    "biocViews": [
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    "Description": "Starr facilitates the analysis of ChIP-chip data, in particular that of Affymetrix tiling arrays. The package provides functions for data import, quality assessment, data visualization and exploration. Furthermore, it includes high-level analysis features like association of ChIP signals with annotated features, correlation analysis of ChIP signals and other genomic data (e.g. gene expression), peak-finding with the CMARRT algorithm and comparative display of multiple clusters of ChIP-profiles. It uses the basic Bioconductor classes ExpressionSet and probeAnno for maximum compatibility with other software on Bioconductor. All functions from Starr can be used to investigate preprocessed data from the Ringo package, and vice versa. An important novel tool is the the automated generation of correct, up-to-date microarray probe annotation (bpmap) files, which relies on an efficient mapping of short sequences (e.g. the probe sequences on a microarray) to an arbitrary genome.",
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      "limma"
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    "Version": "1.8.0",
    "Maintainer": "J. Zhang <jzhang@jimmy.harvard.edu>",
    "Author": "J. Zhang and B. Feng",
    "Title": "Find chromosome regions showing common gains/losses",
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    "Package": "cghMCR",
    "vignettes": [
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    "biocViews": [
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      "Microarray",
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      "Software"
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      "Biobase (>= 2.5.5)"
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    "Author": "R. Alvarez-Gonzalez, D. Glez-Pena, F. Diaz, F. Fdez-Riverola",
    "Title": "Gene Selection",
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    "vignettes": [
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    "biocViews": [
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      "Microarray",
      "Software"
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    "Description": "This package provides a supervised technique able to identify differentially expressed genes, based on the construction of \\emph{Fuzzy Patterns} (FPs). The Fuzzy Patterns are built by means of applying 3 Membership Functions to discretized gene expression values.",
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    "Author": "Pan Du, Warren Kibbe, Simon Lin",
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    "Archs": "i386, x64",
    "License": "LGPL (>= 2)",
    "biocViews": [
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      "Proteomics",
      "Software"
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    "Description": "Processing Mass Spectrometry spectrum by using wavelet based algorithm",
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    "Author": "A. Zackay, C. Steinhoff",
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    "Imports": [
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      "ca",
      "graphics",
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      "grid",
      "gridBase",
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      "stats",
      "utils"
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    "License": "GPL (>= 2)",
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      "Clustering",
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    "Maintainer": "Kasper Daniel Hansen <khansen@stat.berkeley.edu>",
    "Author": "Henrik Bengtsson, James Bullard, Robert Gentleman, Kasper Daniel Hansen, Martin Morgan",
    "Title": "Affymetrix File Parsing SDK",
    "source.ver": "src/contrib/affxparser_1.22.1.tar.gz",
    "Suggests": [
      "R.utils",
      "AffymetrixDataTestFiles"
    ],
    "Package": "affxparser",
    "Archs": "i386, x64",
    "License": "LGPL (>= 2)",
    "biocViews": [
      "DataImport",
      "Infrastructure",
      "Software"
    ],
    "Description": "Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR).  It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files are supported.  Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL).  These files can be read either in full or in part.  For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure.",
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      "affyILM",
      "AffyTiling",
      "GeneRegionScan",
      "ITALICS",
      "oligo"
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    "win.binary.ver": "bin/windows/contrib/2.12/affxparser_1.22.1.zip"
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      "R (>= 2.5.1)",
      "methods",
      "stats",
      "Biobase"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/CMA_1.8.1.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/CMA_1.8.1.tgz",
    "Version": "1.8.1",
    "Maintainer": "Christoph Bernau <bernau@ibe.med.uni-muenchen.de>",
    "Author": "Martin Slawski <ms@cs.uni-sb.de>, Anne-Laure Boulesteix <boulesteix@ibe.med.uni-muenchen.de>, Christoph Bernau <bernau@ibe.med.uni-muenchen.de>.",
    "Title": "Synthesis of microarray-based classification",
    "source.ver": "src/contrib/CMA_1.8.1.tar.gz",
    "Suggests": [
      "MASS",
      "class",
      "nnet",
      "glmnet",
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      "plsgenomics",
      "gbm",
      "mgcv",
      "corpcor",
      "limma",
      "st"
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    "Package": "CMA",
    "vignettes": [
      "vignettes/CMA/inst/doc/CMA_vignette.pdf"
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    "License": "GPL (>= 2)",
    "biocViews": [
      "Classification",
      "Software",
      "Statistics"
    ],
    "Description": "This package provides a comprehensive collection of various microarray-based classification algorithms both from Machine Learning and Statistics. Variable Selection, Hyperparameter tuning, Evaluation and Comparison can be performed combined or stepwise in a user-friendly environment.",
    "win.binary.ver": "bin/windows/contrib/2.12/CMA_1.8.1.zip"
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      "R (>= 2.12.0)",
      "BSgenome"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/MEDIPS_1.0.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/MEDIPS_1.0.0.tgz",
    "Version": "1.0.0",
    "Maintainer": "Lukas Chavez <chavez@molgen.mpg.de>",
    "Author": "Lukas Chavez, Joern Dietrich",
    "Title": "MeDIP-Seq data analysis",
    "source.ver": "src/contrib/MEDIPS_1.0.0.tar.gz",
    "Imports": [
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      "BSgenome",
      "graphics",
      "gtools",
      "IRanges",
      "methods",
      "stats",
      "utils"
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    "Suggests": [
      "BSgenome",
      "BSgenome.Hsapiens.UCSC.hg19"
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    "Package": "MEDIPS",
    "vignettes": [
      "vignettes/MEDIPS/inst/doc/MEDIPS.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL (>=2)",
    "biocViews": [
      "Sequencing",
      "Software"
    ],
    "Description": "MEDIPS was developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-Seq). Nevertheless, functionalities like the quality controls may be applied to other types of sequencing data (e.g. ChIP-Seq). MEDIPS adresses several aspects in the context of MeDIP-Seq data analysis.",
    "win.binary.ver": "bin/windows/contrib/2.12/MEDIPS_1.0.0.zip"
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    "Depends": [
      "R (>= 1.7.0)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/impute_1.24.0.zip",
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    "Version": "1.24.0",
    "Maintainer": "Balasubramanian Narasimhan <naras@stat.Stanford.EDU>",
    "Author": "Trevor Hastie, Robert Tibshirani, Balasubramanian Narasimhan, Gilbert Chu",
    "Title": "impute: Imputation for microarray data",
    "suggestsMe": [
      "BioNet"
    ],
    "source.ver": "src/contrib/impute_1.24.0.tar.gz",
    "Package": "impute",
    "Archs": "i386, x64",
    "License": "GPL-2",
    "biocViews": [
      "Bioinformatics",
      "Microarray",
      "Software"
    ],
    "Description": "Imputation for microarray data (currently KNN only)",
    "win.binary.ver": "bin/windows/contrib/2.12/impute_1.24.0.zip"
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    "Depends": [
      "R (>= 2.8.0)",
      "Biobase (>= 2.5.5)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/affy_1.28.1.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/affy_1.28.0.tgz",
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      "affycoretools",
      "affydata",
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      "affylmGUI",
      "affyPara",
      "affypdnn",
      "affyPLM",
      "affyQCReport",
      "AgiMicroRna",
      "ALLMLL",
      "altcdfenvs",
      "AmpAffyExample",
      "arrayMvout",
      "ArrayTools",
      "bgx",
      "bronchialIL13",
      "CLL",
      "dualKS",
      "ecoliLeucine",
      "estrogen",
      "exonmap",
      "farms",
      "gcrma",
      "LMGene",
      "logitT",
      "LVSmiRNA",
      "maDB",
      "MAQCsubset",
      "MAQCsubsetAFX",
      "mvoutData",
      "panp",
      "plw",
      "puma",
      "pumadata",
      "qpcrNorm",
      "RefPlus",
      "rHVDM",
      "RPA",
      "simpleaffy",
      "SpikeIn",
      "SpikeInSubset",
      "sscore",
      "Starr",
      "webbioc",
      "XhybCasneuf"
    ],
    "Maintainer": "Rafael A. Irizarry <rafa@jhu.edu>",
    "Author": "Rafael A. Irizarry <rafa@jhu.edu>, Laurent Gautier <lgautier@gmail.com>, Benjamin Milo Bolstad <bmb@bmbolstad.com>, and Crispin Miller <cmiller@picr.man.ac.uk> with contributions from Magnus Astrand <Magnus.Astrand@astrazeneca.com>, Leslie M. Cope <cope@mts.jhu.edu>, Robert Gentleman, Jeff Gentry, Conrad Halling <challing@agilixcorp.com>, Wolfgang Huber, James MacDonald <jmacdon@med.umich.edu>, Benjamin I. P. Rubinstein, Christopher Workman <workman@cbs.dtu.dk>, John Zhang",
    "Title": "Methods for Affymetrix Oligonucleotide Arrays",
    "suggestsMe": [
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      "beadarray",
      "beadarraySNP",
      "BiocCaseStudies",
      "Biostrings",
      "BufferedMatrixMethods",
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      "ExpressionView",
      "factDesign",
      "GeneRegionScan",
      "hexbin",
      "limma",
      "made4",
      "oneChannelGUI",
      "siggenes"
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    "source.ver": "src/contrib/affy_1.28.1.tar.gz",
    "Imports": [
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      "Biobase (>= 2.5.5)",
      "graphics",
      "grDevices",
      "methods",
      "preprocessCore",
      "stats",
      "utils"
    ],
    "Suggests": [
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      "affydata"
    ],
    "Package": "affy",
    "vignettes": [
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      "vignettes/affy/inst/doc/builtinMethods.pdf",
      "vignettes/affy/inst/doc/customMethods.pdf",
      "vignettes/affy/inst/doc/vim.pdf"
    ],
    "Archs": "i386, x64",
    "License": "LGPL (>= 2.0)",
    "LinkingTo": "preprocessCore",
    "biocViews": [
      "Microarray",
      "OneChannel",
      "Preprocessing",
      "Software"
    ],
    "Description": "The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.",
    "importsMe": [
      "affyILM",
      "affyQCReport",
      "AffyTiling",
      "ArrayExpress",
      "arrayQualityMetrics",
      "ArrayTools",
      "farms",
      "frma",
      "frmaTools",
      "gcrma",
      "GEOsubmission",
      "Harshlight",
      "HTqPCR",
      "lumi",
      "makecdfenv",
      "plier",
      "plw",
      "puma",
      "simpleaffy",
      "tilingArray",
      "vsn"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/affy_1.28.1.zip"
  },
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      "affy (>= 1.5)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/affypdnn_1.24.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/affypdnn_1.24.0.tgz",
    "Version": "1.24.0",
    "Maintainer": "Laurent Gautier<lgautier@gmail.com>",
    "Author": "H. Bjorn Nielsen and Laurent Gautier (Many thanks to Li Zhang early communications about the existence of the PDNN program and related publications).",
    "Title": "Probe Dependent Nearest Neighbours (PDNN) for the affy package",
    "source.ver": "src/contrib/affypdnn_1.24.0.tar.gz",
    "Suggests": [
      "affydata",
      "hgu95av2probe"
    ],
    "Package": "affypdnn",
    "vignettes": [
      "vignettes/affypdnn/inst/doc/affypdnn.pdf"
    ],
    "License": "LGPL",
    "biocViews": [
      "Microarray",
      "OneChannel",
      "Preprocessing",
      "Software"
    ],
    "Description": "The package contains functions to perform the PDNN method described by Li Zhang et al.",
    "win.binary.ver": "bin/windows/contrib/2.12/affypdnn_1.24.0.zip"
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  "tilingArray": {
    "Depends": [
      "R (>= 2.11.0)",
      "Biobase",
      "methods",
      "pixmap"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/tilingArray_1.28.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/tilingArray_1.28.0.tgz",
    "Version": "1.28.0",
    "dependsOnMe": [
      "ADaCGH2",
      "davidTiling"
    ],
    "Maintainer": "Zhenyu Xu <zhenyu@ebi.ac.uk>",
    "Author": "Wolfgang Huber, Zhenyu Xu, Joern Toedling with contributions from Matt Ritchie",
    "Title": "Transcript mapping with high-density oligonucleotide tiling arrays",
    "source.ver": "src/contrib/tilingArray_1.28.0.tar.gz",
    "Imports": [
      "strucchange",
      "affy",
      "vsn",
      "genefilter",
      "RColorBrewer",
      "grid"
    ],
    "Package": "tilingArray",
    "vignettes": [
      "vignettes/tilingArray/inst/doc/assessNorm.pdf",
      "vignettes/tilingArray/inst/doc/costMatrix.pdf",
      "vignettes/tilingArray/inst/doc/findsegments.pdf",
      "vignettes/tilingArray/inst/doc/plotAlongChrom.pdf",
      "vignettes/tilingArray/inst/doc/segmentation.pdf"
    ],
    "Archs": "i386, x64",
    "License": "Artistic-2.0",
    "biocViews": [
      "Microarray",
      "OneChannel",
      "Preprocessing",
      "Software",
      "Visualization"
    ],
    "Description": "The package provides functionality that can be useful for the analysis of high-density tiling microarray data (such as from Affymetrix genechips) for measuring transcript abundance and architecture. The main functionalities of the package are: 1. the class 'segmentation' for representing partitionings of a linear series of data; 2. the function 'segment' for fitting piecewise constant models using a dynamic programming algorithm that is both fast and exact; 3. the function 'confint' for calculating confidence intervals using the strucchange package; 4. the function 'plotAlongChrom' for generating pretty plots; 5. the function 'normalizeByReference' for probe-sequence dependent response adjustment from a (set of) reference hybridizations.",
    "importsMe": [
      "snapCGH"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/tilingArray_1.28.0.zip"
  },
  "metaArray": {
    "win64.binary.ver": "bin/windows64/contrib/2.12/metaArray_1.26.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/metaArray_1.26.0.tgz",
    "Version": "1.26.0",
    "Maintainer": "Hyungwon Choi <hwchoi@umich.edu>",
    "Author": "Debashis Ghosh <ghoshd@umich.edu> Hyungwon Choi <hwchoi@umich.edu>",
    "Title": "Integration of Microarray Data for Meta-analysis",
    "suggestsMe": [
      "oneChannelGUI"
    ],
    "source.ver": "src/contrib/metaArray_1.26.0.tar.gz",
    "Imports": [
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      "MergeMaid",
      "graphics",
      "stats"
    ],
    "Package": "metaArray",
    "vignettes": [
      "vignettes/metaArray/inst/doc/metaArray.pdf"
    ],
    "Archs": "i386, x64",
    "License": "LGPL-2",
    "biocViews": [
      "Bioinformatics",
      "DifferentialExpression",
      "Microarray",
      "Software"
    ],
    "Description": "1) Data transformation for meta-analysis of microarray Data: Transformation of gene expression data to signed probability scale (MCMC/EM methods) 2) Combined differential expression on raw scale: Weighted Z-score after stabilizing mean-variance relation within platform",
    "win.binary.ver": "bin/windows/contrib/2.12/metaArray_1.26.0.zip"
  },
  "GeneticsDesign": {
    "win64.binary.ver": "bin/windows64/contrib/2.12/GeneticsDesign_1.18.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/GeneticsDesign_1.18.0.tgz",
    "Version": "1.18.0",
    "Maintainer": "The R Genetics Project <r-genetics-talk@lists.sourceforge.net>",
    "Author": "Gregory Warnes <warnes@bst.rochester.edu> David Duffy <davidD@qumr.edu.au>, Michael Man <michael.man@pfizer.com> Weiliang Qiu <stwxq@channing.harvard.edu> Ross Lazarus <ross.lazarus@channing.harvard.edu>",
    "Title": "Functions for designing genetics studies",
    "source.ver": "src/contrib/GeneticsDesign_1.18.0.tar.gz",
    "Imports": [
      "gmodels",
      "graphics",
      "gtools (>= 2.4.0)",
      "mvtnorm",
      "stats"
    ],
    "Package": "GeneticsDesign",
    "vignettes": [
      "vignettes/GeneticsDesign/inst/doc/GPC.pdf"
    ],
    "License": "GPL",
    "biocViews": [
      "Genetics",
      "Software"
    ],
    "Description": "This package contains functions useful for designing genetics studies, including power and sample-size calculations.",
    "win.binary.ver": "bin/windows/contrib/2.12/GeneticsDesign_1.18.0.zip"
  },
  "VanillaICE": {
    "Depends": [
      "R (>= 2.10.0)",
      "crlmm (>= 1.5.44)",
      "IRanges",
      "oligoClasses (>= 1.9.53)",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/VanillaICE_1.12.4.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/VanillaICE_1.12.4.tgz",
    "Version": "1.12.4",
    "Maintainer": "Robert Scharpf <rscharpf@jhsph.edu>",
    "Author": "Robert Scharpf <rscharpf@jhsph.edu>, Kevin Scharpf, and Ingo Ruczinski <ingo@jhsph.edu>",
    "Title": "A Hidden Markov Model for high throughput genotyping arrays",
    "suggestsMe": [
      "SNPchip"
    ],
    "source.ver": "src/contrib/VanillaICE_1.12.4.tar.gz",
    "Imports": [
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      "stats"
    ],
    "Suggests": [
      "genomewidesnp6Crlmm",
      "hapmapsnp6",
      "RColorBrewer",
      "genefilter",
      "RSQLite"
    ],
    "Package": "VanillaICE",
    "vignettes": [
      "vignettes/VanillaICE/inst/doc/VanillaICE.pdf"
    ],
    "Archs": "i386, x64",
    "License": "LGPL-2",
    "biocViews": [
      "Bioinformatics",
      "CopyNumberVariants",
      "GeneticVariability",
      "SNP",
      "Software",
      "Visualization"
    ],
    "Description": "Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays",
    "win.binary.ver": "bin/windows/contrib/2.12/VanillaICE_1.12.4.zip"
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      "R (>= 2.8)",
      "affy (>= 1.20.0)",
      "MASS",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/farms_1.2.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/farms_1.2.0.tgz",
    "Version": "1.2.0",
    "URL": "http://www.bioinf.jku.at/software/farms/farms.html",
    "Maintainer": "Djork-Arne Clevert <okko@clevert.de>",
    "Author": "Djork-Arne Clevert <okko@clevert.de>",
    "Title": "FARMS - Factor Analysis for Robust Microarray Summarization",
    "source.ver": "src/contrib/farms_1.2.0.tar.gz",
    "Imports": [
      "affy",
      "MASS",
      "Biobase (>= 1.13.41)",
      "methods",
      "graphics"
    ],
    "Suggests": [
      "affydata",
      "Biobase",
      "utils"
    ],
    "Package": "farms",
    "vignettes": [
      "vignettes/farms/inst/doc/farms.pdf"
    ],
    "License": "LGPL (>= 2.1)",
    "biocViews": [
      "GeneExpression",
      "Microarray",
      "Preprocessing",
      "QualityControl",
      "Software"
    ],
    "Description": "The package provides the summarization algorithm called Factor Analysis for Robust Microarray Summarization (FARMS) and a novel unsupervised feature selection criterion called \"I/NI-calls\"",
    "win.binary.ver": "bin/windows/contrib/2.12/farms_1.2.0.zip"
  },
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      "R (>= 2.11.0)",
      "oligoClasses (>= 1.9.41)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/oligo_1.14.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/oligo_1.14.0.tgz",
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    "dependsOnMe": [
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      "oligoData",
      "pd.081229.hg18.promoter.medip.hx1",
      "pd.2006.07.18.hg18.refseq.promoter",
      "pd.2006.07.18.mm8.refseq.promoter",
      "pd.2006.10.31.rn34.refseq.promoter",
      "pd.charm.hg18.example",
      "pd.cytogenetics.array",
      "pd.feinberg.hg18.me.hx1",
      "pd.feinberg.mm8.me.hx1",
      "pd.genomewidesnp.5",
      "pd.genomewidesnp.6",
      "pd.hg.u95a",
      "pd.hg.u95av2",
      "pd.ht.hg.u133.plus.pm",
      "pd.huex.1.0.st.v2",
      "pd.hugene.1.0.st.v1",
      "pd.hugene.1.1.st.v1",
      "pd.mapping250k.nsp",
      "pd.mapping250k.sty",
      "pd.mapping50k.hind240",
      "pd.mapping50k.xba240",
      "pd.moex.1.0.st.v1",
      "pd.mogene.1.0.st.v1",
      "pd.mogene.1.1.st.v1",
      "pd.mouse430.2",
      "pd.raex.1.0.st.v1",
      "pd.ragene.1.0.st.v1",
      "pd.ragene.1.1.st.v1",
      "pdInfoBuilder"
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    "Maintainer": "Benilton Carvalho <carvalho@bclab.org>",
    "Author": "Benilton Carvalho <carvalho@bclab.org>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber",
    "Title": "Preprocessing tools for oligonucleotide arrays.",
    "suggestsMe": [
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      "hapmap100kxba",
      "hapmap500knsp",
      "hapmap500ksty",
      "hapmapsnp5",
      "hapmapsnp6",
      "maqcExpression4plex"
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    "source.ver": "src/contrib/oligo_1.14.0.tar.gz",
    "Imports": [
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      "affxparser (>= 1.17.3)",
      "Biobase (>= 2.7.3)",
      "DBI (>= 0.2-4)",
      "graphics",
      "methods",
      "preprocessCore (>= 1.9.0)",
      "splines",
      "stats",
      "utils"
    ],
    "Suggests": [
      "hapmap100kxba",
      "pd.mapping50k.xba240",
      "pd.hg18.60mer.expr",
      "maqcExpression4plex",
      "genefilter",
      "limma",
      "RColorBrewer"
    ],
    "Package": "oligo",
    "vignettes": [
      "vignettes/oligo/inst/doc/V1Overview.pdf",
      "vignettes/oligo/inst/doc/V2NExpression.pdf",
      "vignettes/oligo/inst/doc/V3AffySnpGenotype.pdf",
      "vignettes/oligo/inst/doc/V4Experimental.pdf",
      "vignettes/oligo/inst/doc/V5ExonGene.pdf"
    ],
    "Archs": "i386, x64",
    "License": "LGPL (>= 2)",
    "LinkingTo": "preprocessCore",
    "biocViews": [
      "Bioinformatics",
      "ChIPchip",
      "CopyNumberVariants",
      "CpGIsland",
      "DNAMethylation",
      "DataImport",
      "DifferentialExpression",
      "ExonArray",
      "GeneExpression",
      "Microarray",
      "OneChannel",
      "Preprocessing",
      "SNP",
      "Software",
      "Transcription",
      "TwoChannel"
    ],
    "Description": "A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).",
    "Enhances": [
      "ff",
      "snow"
    ],
    "importsMe": [
      "charm",
      "ITALICS",
      "makePlatformDesign"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/oligo_1.14.0.zip"
  },
  "CoCiteStats": {
    "Depends": [
      "R (>= 2.0)",
      "org.Hs.eg.db"
    ],
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    "Version": "1.22.0",
    "Maintainer": "Biocore Team c/o BioC user list <bioconductor@stat.math.ethz.ch>",
    "Author": "B. Ding and R. Gentleman",
    "Title": "Different test statistics based on co-citation.",
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      "Software"
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    "Description": "A collection of software tools for dealing with co-citation data.",
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    "Version": "1.24.0",
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      "webbioc"
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    "Maintainer": "John D. Storey <jstorey@u.washington.edu>",
    "Author": "Alan Dabney <adabney@u.washington.edu> and John D. Storey <jstorey@u.washington.edu>, with assistance from Gregory R. Warnes <gregory_r_warnes@groton.pfizer.com>",
    "Title": "Q-value estimation for false discovery rate control",
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      "tcltk"
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    "Package": "qvalue",
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      "vignettes/qvalue/inst/doc/pHist.pdf",
      "vignettes/qvalue/inst/doc/qHist.pdf",
      "vignettes/qvalue/inst/doc/qPlots.pdf",
      "vignettes/qvalue/inst/doc/qvalue-002.pdf",
      "vignettes/qvalue/inst/doc/qvalue-004.pdf",
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    "License": "LGPL",
    "biocViews": [
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    "Description": "This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. Various plots are automatically generated, allowing one to make sensible significance cut-offs. Several mathematical results have recently been shown on the conservative accuracy of the estimated q-values from this software. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining.",
    "importsMe": [
      "webbioc"
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    "win.binary.ver": "bin/windows/contrib/2.12/qvalue_1.24.0.zip"
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      "R (>= 2.8.0)",
      "methods"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/fabia_1.2.0.zip",
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    "Version": "1.2.0",
    "URL": "http://www.bioinf.jku.at/software/fabia/fabia.html",
    "Maintainer": "Sepp Hochreiter <hochreit@bioinf.jku.at>",
    "Author": "Sepp Hochreiter <hochreit@bioinf.jku.at>",
    "Title": "FABIA: Factor Analysis for Bicluster Acquisition",
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    "Archs": "i386, x64",
    "License": "LGPL (>= 2.1)",
    "biocViews": [
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    "Description": "Biclustering by \"Factor Analysis for Bicluster Acquisition\" (FABIA). FABIA is a model-based technique for biclustering, that is clustering rows and columns simultaneously. Biclusters are found by factor analysis where both the factors and the loading matrix are sparse. FABIA is a multiplicative model that extracts linear dependencies between samples and feature patterns. It captures realistic non-Gaussian data distributions with heavy tails as observed in gene expression measurements. FABIA utilizes well understood model selection techniques like the EM algorithm and variational approaches and is embedded into a Bayesian framework. FABIA ranks biclusters according to their information content and separates spurious biclusters from true biclusters. The code is written in C++ based on Rcpp package.",
    "win.binary.ver": "bin/windows/contrib/2.12/fabia_1.2.0.zip"
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    "Depends": [
      "R (>= 2.10.0)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/iSeq_1.0.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/iSeq_1.0.0.tgz",
    "Version": "1.0.0",
    "Maintainer": "Qianxing Mo <moq@mskcc.org>",
    "Author": "Qianxing Mo",
    "Title": "Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models",
    "source.ver": "src/contrib/iSeq_1.0.0.tar.gz",
    "Package": "iSeq",
    "vignettes": [
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    "Archs": "i386, x64",
    "License": "GPL (>= 2)",
    "biocViews": [
      "ChIP-seq",
      "Software",
      "bioinformatics",
      "massively parallel sequencing",
      "next generation sequencing"
    ],
    "Description": "This package uses Bayesian hidden Ising models to identify IP-enriched genomic regions from ChIP-seq data. It can be used to analyze the ChIP-seq data with or without controls.",
    "win.binary.ver": "bin/windows/contrib/2.12/iSeq_1.0.0.zip"
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      "Biobase",
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    "win64.binary.ver": "bin/windows64/contrib/2.12/flowCore_1.16.0.zip",
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    "Author": "B. Ellis, P. Haaland, F. Hahne, N. Le Meur, N. Gopalakrishnan",
    "Title": "flowCore: Basic structures for flow cytometry data",
    "source.ver": "src/contrib/flowCore_1.16.0.tar.gz",
    "Imports": [
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      "feature",
      "graph",
      "graphics",
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      "rrcov",
      "stats",
      "utils"
    ],
    "Suggests": [
      "Rgraphviz",
      "flowViz",
      "ncdf"
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    "Package": "flowCore",
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    "Archs": "i386, x64",
    "License": "Artistic-2.0",
    "biocViews": [
      "CellBasedAssays",
      "Flowcytometry",
      "Infrastructure",
      "Software"
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    "Description": "Provides S4 data structures and basic functions to deal with flow cytometry data.",
    "importsMe": [
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      "flowFP",
      "flowMeans",
      "flowMerge",
      "flowQ",
      "flowStats",
      "flowTrans",
      "flowUtils",
      "flowViz",
      "plateCore"
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    "win.binary.ver": "bin/windows/contrib/2.12/flowCore_1.16.0.zip"
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      "KernSmooth"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/BGmix_1.10.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/BGmix_1.10.0.tgz",
    "Version": "1.10.0",
    "Maintainer": "Alex Lewin <a.m.lewin@imperial.ac.uk>",
    "Author": "Alex Lewin, Natalia Bochkina",
    "Title": "Bayesian models for differential gene expression",
    "source.ver": "src/contrib/BGmix_1.10.0.tar.gz",
    "Package": "BGmix",
    "vignettes": [
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    "Archs": "i386",
    "License": "GPL",
    "biocViews": [
      "DifferentialExpression",
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      "MultipleComparisons",
      "Software"
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    "Description": "Fully Bayesian mixture models for differential gene expression",
    "win.binary.ver": "bin/windows/contrib/2.12/BGmix_1.10.0.zip"
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      "IRanges"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/biocDatasets_1.6.0.zip",
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    "Version": "1.6.0",
    "Maintainer": "L. Gautier <laurent@cbs.dtu.dk>",
    "Author": "L. Gautier",
    "Title": "Synthetic datasets for bioconductor",
    "source.ver": "src/contrib/biocDatasets_1.6.0.tar.gz",
    "Imports": [
      "stats",
      "Biostrings",
      "IRanges"
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    "Suggests": [
      "Biobase"
    ],
    "Package": "biocDatasets",
    "vignettes": [
      "vignettes/biocDatasets/inst/doc/synthetic_arrays.pdf"
    ],
    "License": "GPL-3",
    "biocViews": [
      "Infrastructure",
      "Software"
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    "Description": "Synthetic datasets to a) demonstrate the usage of bioconductor packages, b) write unit tests, while keeping dependencies and ressources usage minimal.",
    "win.binary.ver": "bin/windows/contrib/2.12/biocDatasets_1.6.0.zip"
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      "methods",
      "xcms (>= 1.13.5)"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/CAMERA_1.6.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/CAMERA_1.6.0.tgz",
    "Version": "1.6.0",
    "URL": "http://msbi.ipb-halle.de/msbi/CAMERA/",
    "Maintainer": "Carsten Kuhl <ckuhl@ipb-halle.de>",
    "Author": "Carsten Kuhl, Ralf Tautenhahn, Steffen Neumann {ckuhl|rtautenh|sneumann}@ipb-halle.de",
    "Title": "Collection of annotation related methods for mass spectrometry data",
    "source.ver": "src/contrib/CAMERA_1.6.0.tar.gz",
    "Imports": [
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      "xcms",
      "RBGL",
      "graph",
      "graphics",
      "grDevices",
      "stats",
      "utils",
      "Hmisc"
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    "Suggests": [
      "faahKO"
    ],
    "Package": "CAMERA",
    "vignettes": [
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    ],
    "Archs": "i386, x64",
    "License": "GPL (>= 2)",
    "biocViews": [
      "MassSpectrometry",
      "Software",
      "Technology"
    ],
    "Description": "Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, EIC correlation based tagging of unknown adducts and fragments",
    "win.binary.ver": "bin/windows/contrib/2.12/CAMERA_1.6.0.zip"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/Heatplus_1.20.0.tgz",
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    "Maintainer": "Alexander Ploner <Alexander.Ploner@ki.se>",
    "Author": "Alexander Ploner <Alexander.Ploner@ki.se>",
    "Title": "A heat map displaying covariates and coloring clusters",
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    "Imports": [
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      "grDevices",
      "stats"
    ],
    "Package": "Heatplus",
    "vignettes": [
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    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "Microarray",
      "Software",
      "Visualization"
    ],
    "Description": "Add an extra graphical display at the bottom of a heat map, indicating for each column a) whether it has one of several binary properties or not, and b) the value of a quantitative variable. A cutting threshold for the sample dendrogram can also be specified, and the resulting clustering of the columns is indicated by coloring both the dendrogram and the extra variable display.",
    "win.binary.ver": "bin/windows/contrib/2.12/Heatplus_1.20.0.zip"
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      "locfit"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/DESeq_1.2.1.zip",
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    "Version": "1.2.1",
    "URL": "http://www-huber.embl.de/users/anders/DESeq/",
    "Maintainer": "Simon Anders <sanders@fs.tum.de>",
    "Author": "Simon Anders, EMBL Heidelberg <sanders@fs.tum.de>",
    "Title": "Digital gene expresion analysis based on the negative binomial distribution",
    "source.ver": "src/contrib/DESeq_1.2.1.tar.gz",
    "Imports": [
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      "geneplotter",
      "methods"
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    "Package": "DESeq",
    "vignettes": [
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    ],
    "Archs": "i386, x64",
    "License": "GPL (>= 3)",
    "biocViews": [
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      "DifferentialExpression",
      "HighThroughputSequencing",
      "RNAseq",
      "SAGE",
      "Software"
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    "Description": "Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution",
    "importsMe": [
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    "win.binary.ver": "bin/windows/contrib/2.12/DESeq_1.2.1.zip"
  },
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      "quantreg",
      "splines",
      "MASS",
      "limma",
      "affy",
      "methods",
      "SparseM",
      "vsn"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/LVSmiRNA_1.0.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/LVSmiRNA_1.0.0.tgz",
    "Version": "1.0.0",
    "Maintainer": "Stefano Calza <stefano.calza@biostatistics.it>",
    "Author": "Stefano Calza, Suo Chen, Yudi Pawitam",
    "Title": "LVS normalization for Agilent miRNA data",
    "source.ver": "src/contrib/LVSmiRNA_1.0.0.tar.gz",
    "Package": "LVSmiRNA",
    "vignettes": [
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    "Archs": "i386, x64",
    "License": "GPL2",
    "biocViews": [
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      "OneChannel",
      "Preprocessing",
      "Software"
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    "Description": "Normalization of Agilent miRNA arrays.",
    "Enhances": [
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      "snow",
      "Rmpi"
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    "win.binary.ver": "bin/windows/contrib/2.12/LVSmiRNA_1.0.0.zip"
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    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/CSAR_1.2.0.zip",
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    "Version": "1.2.0",
    "Maintainer": "Jose M Muino <jose.muino@wur.nl>",
    "Author": "Jose M Muino",
    "Title": "Statistical tools for the analysis of ChIP-seq data",
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    "Imports": [
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      "utils"
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    "Suggests": [
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    "Archs": "i386, x64",
    "License": "Artistic-2.0",
    "biocViews": [
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      "Genetics",
      "Software",
      "Transcription"
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    "Description": "Statistical tools for ChIP-seq data analysis. The package includes the statistical method described in Kaufmann et al. (2009) PLoS Biology: 7(4):e1000090. Briefly, Taking the average DNA fragment size subjected to sequencing into account, the software calculates genomic single-nucleotide read-enrichment values. After normalization, sample and control are compared using a test based on the Poisson distribution. Test statistic thresholds to control the false discovery rate are obtained through random permutation.",
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/daMA_1.22.0.tgz",
    "Version": "1.22.0",
    "URL": "http://www.microarrays.med.uni-goettingen.de",
    "Maintainer": "Jobst Landgrebe <jlandgr1@gwdg.de>",
    "Author": "Jobst Landgrebe <jlandgr1@gwdg.de> and Frank Bretz <bretz@bioinf.uni-hannover.de>",
    "Title": "Efficient design and analysis of factorial two-colour microarray data",
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    "Imports": [
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      "stats"
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    "Package": "daMA",
    "License": "GPL (>= 2)",
    "biocViews": [
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      "DifferentialExpression",
      "Microarray",
      "Software",
      "TwoChannel"
    ],
    "Description": "This package contains functions for the efficient design of factorial two-colour microarray experiments and for the statistical analysis of factorial microarray data. Statistical details are described in Bretz et al. (2003, submitted)",
    "win.binary.ver": "bin/windows/contrib/2.12/daMA_1.22.0.zip"
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      "GO.db",
      "org.Hs.eg.db"
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    "Version": "1.8.3",
    "Maintainer": "Guangchuang Yu <guangchuangyu@gmail.com>",
    "Author": "Guangchuang Yu",
    "Title": "GO-terms Semantic Similarity Measures",
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    "Suggests": [
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      "org.At.tair.db",
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      "org.Ce.eg.db",
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      "org.Dm.eg.db",
      "org.Dr.eg.db",
      "org.EcK12.eg.db",
      "org.EcSakai.eg.db",
      "org.Gg.eg.db",
      "org.Mm.eg.db",
      "org.Mmu.eg.db",
      "org.Pf.plasmo.db",
      "org.Pt.eg.db",
      "org.Rn.eg.db",
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    "License": "GPL-2",
    "biocViews": [
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      "Bos_taurus",
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      "Danio_rerio",
      "Drosophila_melanogaster",
      "Escherichia_coli",
      "GO",
      "Gallus_gallus",
      "Homo_sapiens",
      "Mus_musculus",
      "Pan_troglodytes",
      "Pathways",
      "Plasmodium_falciparum",
      "Rattus_norvegicus",
      "Saccharomyces_cerevisiae",
      "Software",
      "Streptomyces_coelicolor",
      "Sus_scrofa",
      "Xenopus_laevis"
    ],
    "Description": "Implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for estimating GO semantic similarities. Support many species, including Anopheles, Arabidopsis, Bovine, Canine, Chicken, Chimp, Coelicolor, E coli strain K12 and Sakai, Fly, Human, Malaria, Mouse, Pig, Rhesus, Rat, Worm, Xenopus, Yeast, and Zebrafish.",
    "win.binary.ver": "bin/windows/contrib/2.12/GOSemSim_1.8.3.zip"
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      "RSQLite"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/GEOmetadb_1.10.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/GEOmetadb_1.10.0.tgz",
    "Version": "1.10.0",
    "URL": "http://gbnci.abcc.ncifcrf.gov/geo/",
    "Maintainer": "Jack Zhu <zhujack@mail.nih.gov>",
    "Author": "Jack Zhu and Sean Davis",
    "Title": "A compilation of metadata from NCBI GEO",
    "source.ver": "src/contrib/GEOmetadb_1.10.0.tar.gz",
    "Package": "GEOmetadb",
    "vignettes": [
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      "vignettes/GEOmetadb/inst/doc/GEOmetadb.pdf"
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    "License": "Artistic-2.0",
    "biocViews": [
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      "Software"
    ],
    "Description": "The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data of interest can be challenging using current tools. GEOmetadb is an attempt to make access to the metadata associated with samples, platforms, and datasets much more feasible. This is accomplished by parsing all the NCBI GEO metadata into a SQLite database that can be stored and queried locally. GEOmetadb is simply a thin wrapper around the SQLite database along with associated documentation. Finally, the SQLite database is updated regularly as new data is added to GEO and can be downloaded at will for the most up-to-date metadata. GEOmetadb paper: http://bioinformatics.oxfordjournals.org/cgi/content/short/24/23/2798 .",
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      "stats",
      "multtest",
      "methods"
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    "Author": "Marc Johannes, Markus Ruschhaupt, Holger Froehlich, Ulrich Mansmann, Andreas Buness, Patrick Warnat, Wolfgang Huber, Axel Benner, Tim Beissbarth",
    "Title": "Misclassification error estimation with cross-validation",
    "source.ver": "src/contrib/MCRestimate_2.6.0.tar.gz",
    "Imports": [
      "e1071 (>= 1.5-12)",
      "pamr (>= 1.22)",
      "randomForest (>= 3.9-6)",
      "RColorBrewer (>= 0.1-3)",
      "Biobase (>= 2.5.5)",
      "graphics",
      "grDevices",
      "stats",
      "utils"
    ],
    "Suggests": [
      "xtable (>= 1.2-1)",
      "ROC (>= 1.8.0)",
      "genefilter (>= 1.12.0)",
      "gpls (>= 1.6.0)"
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    "Package": "MCRestimate",
    "vignettes": [
      "vignettes/MCRestimate/inst/doc/UsingMCRestimate.pdf"
    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "Bioinformatics",
      "Classification",
      "Software"
    ],
    "Description": "This package includes a function for combining preprocessing and classification methods to calculate misclassification errors",
    "win.binary.ver": "bin/windows/contrib/2.12/MCRestimate_2.6.0.zip"
  },
  "CGHbase": {
    "Depends": [
      "R (>= 2.4.0)",
      "methods",
      "Biobase (>= 2.5.5)",
      "marray"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/CGHbase_1.8.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/CGHbase_1.8.0.tgz",
    "Version": "1.8.0",
    "dependsOnMe": [
      "CGHcall",
      "CGHnormaliter",
      "CGHregions"
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    "Maintainer": "Sjoerd Vosse <info@vossewebdevelopment.nl>",
    "Author": "Sjoerd Vosse",
    "Title": "CGHbase: Base functions and classes for arrayCGH data analysis.",
    "source.ver": "src/contrib/CGHbase_1.8.0.tar.gz",
    "Package": "CGHbase",
    "License": "GPL",
    "biocViews": [
      "CopyNumberVariants",
      "Infrastructure",
      "Microarray",
      "Software"
    ],
    "Description": "Contains functions and classes that are needed by arrayCGH packages.",
    "importsMe": [
      "CGHnormaliter"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/CGHbase_1.8.0.zip"
  },
  "GlobalAncova": {
    "Depends": [
      "methods",
      "corpcor",
      "globaltest"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/GlobalAncova_3.18.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/GlobalAncova_3.18.0.tgz",
    "Version": "3.18.0",
    "Maintainer": "R. Meister <meister@tfh-berlin.de>",
    "Author": "U. Mansmann, R. Meister, M. Hummel, R. Scheufele, with contributions from S. Knueppel",
    "Title": "Calculates a global test for differential gene expression between groups",
    "source.ver": "src/contrib/GlobalAncova_3.18.0.tar.gz",
    "Imports": [
      "annotate",
      "AnnotationDbi"
    ],
    "Suggests": [
      "Biobase",
      "annotate",
      "GO.db",
      "KEGG.db",
      "golubEsets",
      "hu6800.db",
      "vsn",
      "GSEABase"
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    "Package": "GlobalAncova",
    "vignettes": [
      "vignettes/GlobalAncova/inst/doc/GlobalAncova.pdf",
      "vignettes/GlobalAncova/inst/doc/GlobalAncovaDecomp.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL (>= 2)",
    "biocViews": [
      "Bioinformatics",
      "DifferentialExpression",
      "Microarray",
      "OneChannel",
      "Pathways",
      "Software"
    ],
    "Description": "We give the following arguments in support of the GlobalAncova approach: After appropriate normalisation, gene-expression-data appear rather symmetrical and outliers are no real problem, so least squares should be rather robust. ANCOVA with interaction yields saturated data modelling e.g. different means per group and gene. Covariate adjustment can help to correct for possible selection bias. Variance homogeneity and uncorrelated residuals cannot be expected. Application of ordinary least squares gives unbiased, but no longer optimal estimates (Gauss-Markov-Aitken). Therefore, using the classical F-test is inappropriate, due to correlation. The test statistic however mirrors deviations from the null hypothesis. In combination with a permutation approach, empirical significance levels can be approximated. Alternatively, an approximation yields asymptotic p-values. This work was supported by the NGFN grant 01 GR 0459, BMBF, Germany.",
    "win.binary.ver": "bin/windows/contrib/2.12/GlobalAncova_3.18.0.zip"
  },
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    "Depends": [
      "R (>= 2.5)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/ecolitk_1.22.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/ecolitk_1.22.0.tgz",
    "Version": "1.22.0",
    "Maintainer": "Laurent Gautier <lgautier@gmail.com>",
    "Author": "Laurent Gautier",
    "Title": "Meta-data and tools for E. coli",
    "source.ver": "src/contrib/ecolitk_1.22.0.tar.gz",
    "Imports": [
      "Biobase",
      "graphics",
      "methods"
    ],
    "Suggests": [
      "ecoliLeucine",
      "ecolicdf",
      "graph",
      "multtest"
    ],
    "Package": "ecolitk",
    "vignettes": [
      "vignettes/ecolitk/inst/doc/ecolitk.pdf"
    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "Annotation",
      "Software",
      "Visualization"
    ],
    "Description": "Meta-data and tools to work with E. coli. The tools are mostly plotting functions to work with circular genomes. They can used with other genomes/plasmids.",
    "win.binary.ver": "bin/windows/contrib/2.12/ecolitk_1.22.0.zip"
  },
  "GLAD": {
    "Depends": [
      "R (>= 2.5.0)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/GLAD_2.12.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/GLAD_2.12.0.tgz",
    "Version": "2.12.0",
    "dependsOnMe": [
      "ITALICS",
      "MANOR"
    ],
    "URL": "http://bioinfo.curie.fr",
    "Maintainer": "Philippe Hupe <glad@curie.fr>",
    "Author": "Philippe Hupe",
    "Title": "Gain and Loss Analysis of DNA",
    "suggestsMe": [
      "ADaCGH2"
    ],
    "source.ver": "src/contrib/GLAD_2.12.0.tar.gz",
    "Suggests": [
      "aws",
      "tcltk"
    ],
    "Package": "GLAD",
    "vignettes": [
      "vignettes/GLAD/inst/doc/GLAD.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL",
    "biocViews": [
      "CopyNumberVariants",
      "Microarray",
      "Software"
    ],
    "Description": "Analysis of array CGH data : detection of breakpoints in genomic profiles and assignment of a status (gain, normal or lost) to each chromosomal regions identified.",
    "SystemRequirements": "gsl. Note: users should have GSL installed. Windows users: 'consult the README file available in the inst directory of the source distribution for necessary configuration instructions'.",
    "importsMe": [
      "ITALICS",
      "MANOR",
      "snapCGH"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/GLAD_2.12.0.zip"
  },
  "pgUtils": {
    "Depends": [
      "R (>= 1.8.0)",
      "methods"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/pgUtils_1.22.0.tgz",
    "Version": "1.22.0",
    "dependsOnMe": [
      "maDB"
    ],
    "Maintainer": "Johannes Rainer <johannes.rainer@tugraz.at>",
    "Author": "Johannes Rainer <johannes.rainer@tugraz.at>",
    "Title": "Utility functions for PostgreSQL databases",
    "source.ver": "src/contrib/pgUtils_1.22.0.tar.gz",
    "Imports": [
      "methods",
      "Rdbi (>= 1.0.2)",
      "RdbiPgSQL (>= 1.0.2)"
    ],
    "Package": "pgUtils",
    "vignettes": [
      "vignettes/pgUtils/inst/doc/pgUtils.pdf"
    ],
    "License": "LGPL (>= 2)",
    "biocViews": [
      "Infrastructure",
      "Software"
    ],
    "Description": "Functions for creating PostgreSQL database tables, with auto incrementing primary keys, selection of foreign keys to allow referential integrity and a logging mechanism."
  },
  "gaga": {
    "Depends": [
      "R (>= 2.5.0)",
      "Biobase",
      "coda"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/gaga_1.10.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/gaga_1.10.0.tgz",
    "Version": "1.10.0",
    "Maintainer": "David Rossell <rosselldavid@gmail.com>",
    "Author": "David Rossell <rosselldavid@gmail.com>.",
    "Title": "GaGa hierarchical model for microarray data analysis",
    "source.ver": "src/contrib/gaga_1.10.0.tar.gz",
    "Package": "gaga",
    "vignettes": [
      "vignettes/gaga/inst/doc/gagamanual.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL (>= 2)",
    "biocViews": [
      "Bioinformatics",
      "Classification",
      "DifferentialExpression",
      "Software"
    ],
    "Description": "This package fits Rossell's generalizations of the Gamma-Gamma hierarchical model for microarray data analysis, which substantially improve the quality of the fit at a low computational cost. The model can be fit via empirical Bayes (Expectation-Maximization and Simulated Annealing) and fully Bayesian techniques (Gibbs and Metropolis-Hastings posterior sampling). Routines are provided to perform differential expression analysis and class prediction.",
    "win.binary.ver": "bin/windows/contrib/2.12/gaga_1.10.0.zip"
  },
  "minet": {
    "Depends": [
      "infotheo"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/minet_3.4.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/minet_3.4.0.tgz",
    "Version": "3.4.0",
    "dependsOnMe": [
      "BUS"
    ],
    "URL": "http://minet.meyerp.com",
    "Maintainer": "Patrick E. Meyer <software@meyerp.com>",
    "Author": "Patrick E. Meyer, Frederic Lafitte, Gianluca Bontempi",
    "Title": "Mutual Information NETworks",
    "source.ver": "src/contrib/minet_3.4.0.tar.gz",
    "Package": "minet",
    "Archs": "i386, x64",
    "License": "file LICENSE",
    "biocViews": [
      "GraphsAndNetworks",
      "Microarray",
      "Software"
    ],
    "Description": "This package implements various algorithms for inferring mutual information networks from data.",
    "win.binary.ver": "bin/windows/contrib/2.12/minet_3.4.0.zip"
  },
  "qpcrNorm": {
    "Depends": [
      "methods",
      "Biobase",
      "limma",
      "affy"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/qpcrNorm_1.8.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/qpcrNorm_1.8.0.tgz",
    "Version": "1.8.0",
    "Maintainer": "Jessica Mar <jess@jimmy.harvard.edu>",
    "Author": "Jessica Mar",
    "Title": "Data-driven normalization strategies for high-throughput qPCR data.",
    "source.ver": "src/contrib/qpcrNorm_1.8.0.tar.gz",
    "Package": "qpcrNorm",
    "vignettes": [
      "vignettes/qpcrNorm/inst/doc/qpcrNorm.pdf"
    ],
    "License": "LGPL (>= 2)",
    "biocViews": [
      "GeneExpression",
      "Preprocessing",
      "Software"
    ],
    "Description": "The package contains functions to perform normalization of high-throughput qPCR data. Basic functions for processing raw Ct data plus functions to generate diagnostic plots are also available.",
    "win.binary.ver": "bin/windows/contrib/2.12/qpcrNorm_1.8.0.zip"
  },
  "hypergraph": {
    "Depends": [
      "R (>= 2.1.0)",
      "methods",
      "graph"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/hypergraph_1.22.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/hypergraph_1.22.0.tgz",
    "Version": "1.22.0",
    "dependsOnMe": [
      "altcdfenvs",
      "hyperdraw",
      "RpsiXML"
    ],
    "Maintainer": "Biocore Team c/o BioC user list <bioconductor@stat.math.ethz.ch>",
    "Author": "Seth Falcon, Robert Gentleman",
    "Title": "A package providing hypergraph data structures",
    "source.ver": "src/contrib/hypergraph_1.22.0.tar.gz",
    "Package": "hypergraph",
    "License": "Artistic-2.0",
    "biocViews": [
      "GraphsAndNetworks",
      "Infrastructure",
      "Software"
    ],
    "Description": "A package that implements some simple capabilities for representing and manipulating hypergraphs.",
    "win.binary.ver": "bin/windows/contrib/2.12/hypergraph_1.22.0.zip"
  },
  "ACME": {
    "Depends": [
      "Biobase (>= 2.5.5)",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/ACME_2.6.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/ACME_2.6.0.tgz",
    "Version": "2.6.0",
    "URL": "http://watson.nci.nih.gov/~sdavis",
    "Maintainer": "Sean Davis <sdavis2@mail.nih.gov>",
    "Author": "Sean Davis <sdavis2@mail.nih.gov>",
    "Title": "Algorithms for Calculating Microarray Enrichment (ACME)",
    "source.ver": "src/contrib/ACME_2.6.0.tar.gz",
    "Imports": [
      "graphics",
      "stats"
    ],
    "Package": "ACME",
    "vignettes": [
      "vignettes/ACME/inst/doc/ACME.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL (>= 2)",
    "biocViews": [
      "Bioinformatics",
      "Software"
    ],
    "Description": "ACME (Algorithms for Calculating Microarray Enrichment) is a set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing \"enrichment\".  It does not rely on a specific array technology (although the array should be a \"tiling\" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods.  It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory.",
    "win.binary.ver": "bin/windows/contrib/2.12/ACME_2.6.0.zip"
  },
  "ADaCGH2": {
    "Depends": [
      "R (>= 2.11.0)",
      "tilingArray",
      "aCGH",
      "waveslim",
      "cluster",
      "snapCGH",
      "snowfall",
      "ff"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/ADaCGH2_1.0.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/ADaCGH2_1.0.0.tgz",
    "Version": "1.0.0",
    "URL": "http://launchpad.net/adacgh, http://wavicgh.bioinfo.cnio.es",
    "Maintainer": "Ramon Diaz-Uriarte <rdiaz02@gmail.com>",
    "Author": "Ramon Diaz-Uriarte <rdiaz02@gmail.com>, Oscar M. Rueda <rueda.om@gmail.com>. Wavelet-based aCGH smoothing code from Li Hsu <lih@fhcrc.org> and Douglas Grove <dgrove@fhcrc.org>. Imagemap code from Barry Rowlingson <B.Rowlingson@lancaster.ac.uk>. HaarSeg code from Erez Ben-Yaacov; downloaded from <http://www.ee.technion.ac.il/people/YoninaEldar/Info/software/HaarSeg.htm>",
    "Title": "Analysis of data from aCGH experiments using parallel computing and ff objects",
    "source.ver": "src/contrib/ADaCGH2_1.0.0.tar.gz",
    "Suggests": [
      "GLAD",
      "DNAcopy",
      "CGHregions",
      "rlecuyer"
    ],
    "Package": "ADaCGH2",
    "vignettes": [
      "vignettes/ADaCGH2/inst/doc/ADaCGH2.pdf"
    ],
    "Archs": "i386",
    "License": "GPL (>= 3)",
    "biocViews": [
      "CopyNumberVariants",
      "Microarray",
      "Software"
    ],
    "Description": "Analysis and plotting of array CGH data. Allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized.",
    "Enhances": [
      "Rmpi",
      "multicore"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/ADaCGH2_1.0.0.zip"
  },
  "RbcBook1": {
    "Depends": [
      "Biobase",
      "graph"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/RbcBook1_1.18.1.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/RbcBook1_1.18.1.tgz",
    "Version": "1.18.1",
    "URL": "http://www.biostat.harvard.edu/~carey",
    "Maintainer": "Vince Carey <stvjc@channing.harvard.edu>",
    "Author": "Vince Carey <stvjc@channing.harvard.edu> and Wolfgang Huber <huber@ebi.ac.uk>",
    "Title": "Support for Springer monograph on Bioconductor",
    "source.ver": "src/contrib/RbcBook1_1.18.1.tar.gz",
    "Package": "RbcBook1",
    "vignettes": [
      "vignettes/RbcBook1/inst/doc/RbcBook1.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "Software"
    ],
    "Description": "tools for building book",
    "win.binary.ver": "bin/windows/contrib/2.12/RbcBook1_1.18.1.zip"
  },
  "SNPchip": {
    "Depends": [
      "R (>= 2.10.0)",
      "Biobase (>= 2.7.4)",
      "methods",
      "oligoClasses (>= 1.9.52)",
      "graphics"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/SNPchip_1.14.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/SNPchip_1.14.0.tgz",
    "Version": "1.14.0",
    "dependsOnMe": [
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    ],
    "URL": "http://www.biostat.jhsph.edu/~iruczins/software/snpchip.html",
    "Maintainer": "Robert Scharpf <rscharpf@jhsph.edu>",
    "Author": "Robert Scharpf <rscharpf@jhsph.edu> and Ingo Ruczinski",
    "Title": "Classes and Methods for high throughput SNP chip data",
    "suggestsMe": [
      "Category"
    ],
    "source.ver": "src/contrib/SNPchip_1.14.0.tar.gz",
    "Imports": [
      "Biobase (>= 2.7.4)",
      "graphics",
      "grDevices",
      "methods",
      "oligoClasses (>= 1.9.52)",
      "stats",
      "utils"
    ],
    "Suggests": [
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      "VanillaICE",
      "RColorBrewer",
      "genefilter",
      "pd.mapping50k.xba240"
    ],
    "Package": "SNPchip",
    "vignettes": [
      "vignettes/SNPchip/inst/doc/SNPchip.pdf"
    ],
    "License": "LGPL (>= 2)",
    "biocViews": [
      "CopyNumberVariants",
      "GeneticVariability",
      "SNP",
      "Software",
      "Visualization"
    ],
    "Description": "This package defines classes and functions for plotting copy number and genotype in high throughput SNP platforms such as Affymetrix and Illumina.  In particular, SNPchip is a useful add-on to the oligo package for visualizing SNP-level estimates after pre-processing.",
    "importsMe": [
      "crlmm",
      "VanillaICE"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/SNPchip_1.14.0.zip"
  },
  "XDE": {
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      "R (>= 2.9.0)",
      "Biobase (>= 2.5.5)",
      "methods",
      "graphics"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/XDE_1.10.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/XDE_1.10.0.tgz",
    "Version": "1.10.0",
    "Maintainer": "Robert Scharpf <rscharpf@jhsph.edu>",
    "Author": "R.B. Scharpf, G. Parmigiani, A.B. Nobel, and H. Tjelmeland",
    "Title": "XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression",
    "source.ver": "src/contrib/XDE_1.10.0.tar.gz",
    "Imports": [
      "Biobase",
      "genefilter",
      "graphics",
      "grDevices",
      "gtools",
      "MergeMaid",
      "methods",
      "stats",
      "utils"
    ],
    "Suggests": [
      "siggenes",
      "genefilter",
      "MASS",
      "RColorBrewer",
      "GeneMeta"
    ],
    "Package": "XDE",
    "vignettes": [
      "vignettes/XDE/inst/doc/XDE.pdf",
      "vignettes/XDE/inst/doc/XdeParameterClass.pdf"
    ],
    "Archs": "i386, x64",
    "License": "LGPL-2",
    "biocViews": [
      "Bioinformatics",
      "DifferentialExpression",
      "Microarray",
      "Software"
    ],
    "Description": "Multi-level model for cross-study detection of differential gene expression.",
    "win.binary.ver": "bin/windows/contrib/2.12/XDE_1.10.0.zip"
  },
  "webbioc": {
    "Depends": [
      "R (>= 1.8.0)",
      "Biobase",
      "affy",
      "multtest",
      "annaffy",
      "vsn",
      "gcrma",
      "qvalue"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/webbioc_1.22.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/webbioc_1.22.0.tgz",
    "Version": "1.22.0",
    "URL": "http://www.bioconductor.org/",
    "Maintainer": "Colin A. Smith <webbioc@colinsmith.org>",
    "Author": "Colin A. Smith <webbioc@colinsmith.org>",
    "Title": "Bioconductor Web Interface",
    "source.ver": "src/contrib/webbioc_1.22.0.tar.gz",
    "Imports": [
      "Biobase",
      "multtest",
      "qvalue",
      "stats",
      "utils"
    ],
    "Package": "webbioc",
    "vignettes": [
      "vignettes/webbioc/inst/doc/demoscript.pdf",
      "vignettes/webbioc/inst/doc/webbioc.pdf"
    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "DifferentialExpression",
      "Infrastructure",
      "Microarray",
      "OneChannel",
      "Software"
    ],
    "Description": "An integrated web interface for doing microarray analysis using several of the Bioconductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by many users. (Currently only Affymetrix oligonucleotide analysis is supported.)",
    "SystemRequirements": "Unix, Perl (>= 5.6.0), Netpbm",
    "win.binary.ver": "bin/windows/contrib/2.12/webbioc_1.22.0.zip"
  },
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    "Depends": [
      "R (>= 2.0.0)",
      "impute(>= 1.8.0)",
      "DNAcopy (>= 1.6.0)",
      "methods",
      "Biobase",
      "CGHbase"
    ],
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      "CGHnormaliter"
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    "Maintainer": "Mark van de Wiel <mark.vdwiel@vumc.nl>",
    "Author": "Sjoerd Vosse and Mark van de Wiel",
    "Title": "Calling aberrations for array CGH tumor profiles.",
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    "Package": "CGHcall",
    "vignettes": [
      "vignettes/CGHcall/inst/doc/CGHcall.pdf"
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    "License": "GPL (http://www.gnu.org/copyleft/gpl.html)",
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      "DNACopyNumber",
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    "Description": "Calls aberrations for array CGH data using a six state mixture model as well as several biological concepts that are ignored by existing algorithms. Visualization of profiles is also provided.",
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      "methods",
      "Biobase (>= 2.9.0)",
      "oligoClasses (>= 1.11.7)"
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    "Version": "1.8.11",
    "dependsOnMe": [
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    "Maintainer": "Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>",
    "Author": "Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>, Ingo Ruczinski <iruczins@jhsph.edu>, Rafael A Irizarry",
    "Title": "Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.",
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      "ff",
      "genefilter",
      "mvtnorm",
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    "Suggests": [
      "hapmapsnp6",
      "genomewidesnp6Crlmm (>= 1.0.2)",
      "snpMatrix",
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    "Package": "crlmm",
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      "vignettes/crlmm/inst/doc/copynumber.pdf",
      "vignettes/crlmm/inst/doc/crlmmDownstream.pdf",
      "vignettes/crlmm/inst/doc/crlmmIllumina.pdf",
      "vignettes/crlmm/inst/doc/genotyping.pdf",
      "vignettes/crlmm/inst/doc/illumina_copynumber.pdf"
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    "Archs": "i386, x64",
    "License": "Artistic-2.0",
    "biocViews": [
      "Bioinformatics",
      "CopyNumberVariants",
      "Microarray",
      "Preprocessing",
      "SNP",
      "Software"
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    "Description": "Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms",
    "win.binary.ver": "bin/windows/contrib/2.12/crlmm_1.8.11.zip"
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      "R (>= 2.5.0)",
      "methods",
      "graph",
      "Biobase"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/Rtreemix_1.12.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/Rtreemix_1.12.0.tgz",
    "Version": "1.12.0",
    "Maintainer": "Jasmina Bogojeska <jasmina@mpi-inf.mpg.de>",
    "Author": "Jasmina Bogojeska",
    "Title": "Rtreemix: Mutagenetic trees mixture models.",
    "source.ver": "src/contrib/Rtreemix_1.12.0.tar.gz",
    "Imports": [
      "methods",
      "graph",
      "Biobase",
      "Hmisc"
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    "Suggests": [
      "Rgraphviz"
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    "Package": "Rtreemix",
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      "vignettes/Rtreemix/inst/doc/ExtendedVignette.pdf",
      "vignettes/Rtreemix/inst/doc/Rtreemix.pdf",
      "vignettes/Rtreemix/inst/doc/topologies.pdf"
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    "Archs": "i386, x64",
    "License": "LGPL",
    "biocViews": [
      "Bioinformatics",
      "Software"
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    "Description": "Rtreemix is a package that offers an environment for estimating the mutagenetic trees mixture models from cross-sectional data and using them for various predictions. It includes functions for fitting the trees mixture models, likelihood computations, model comparisons, waiting time estimations, stability analysis, etc.",
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      "R (>= 2.0.0)",
      "grDevices",
      "Biobase",
      "amap"
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    "Maintainer": "Sarah Song <qson003@stat.auckland.ac.nz>",
    "Author": "Sarah Song, Mik Black",
    "Title": "Principal Coordinates and Hotelling's T-Square method",
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    "Suggests": [
      "multtest",
      "hu6800.db",
      "KEGG.db",
      "mvtnorm"
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      "vignettes/pcot2/inst/doc/pcot2.pdf"
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    "biocViews": [
      "DifferentialExpression",
      "Microarray",
      "Software"
    ],
    "Description": "PCOT2 is a permutation-based method for investigating changes in the activity of multi-gene networks. It utilizes inter-gene correlation information to detect significant alterations in gene network activities. Currently it can be applied to two-sample comparisons.",
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      "methods",
      "Biobase (>= 2.5.5)",
      "quantsmooth"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/beadarraySNP_1.16.0.tgz",
    "Version": "1.16.0",
    "Maintainer": "Jan Oosting <j.oosting@lumc.nl>",
    "Author": "Jan Oosting",
    "Title": "Normalization and reporting of Illumina SNP bead arrays",
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    "Suggests": [
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      "affy",
      "limma",
      "snapCGH",
      "beadarray",
      "DNAcopy"
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    "Package": "beadarraySNP",
    "vignettes": [
      "vignettes/beadarraySNP/inst/doc/beadarraySNP.pdf"
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    "License": "GPL-2",
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      "CopyNumberVariants",
      "DataImport",
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      "Preprocessing",
      "SNP",
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    "Description": "Importing data from Illumina SNP experiments and performing copy number calculations and reports.",
    "win.binary.ver": "bin/windows/contrib/2.12/beadarraySNP_1.16.0.zip"
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      "Biobase (>= 2.5.5)",
      "affy (>= 1.23.4)",
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/maDB_1.22.0.tgz",
    "Version": "1.22.0",
    "Maintainer": "Johannes Rainer <johannes.rainer@i-med.ac.at>",
    "Author": "Johannes Rainer <johannes.rainer@i-med.ac.at>",
    "Title": "Microarray database and utility functions for microarray data analysis.",
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    "Suggests": [
      "annaffy (>= 1.6.2)",
      "biomaRt (>= 1.8.2)",
      "geneplotter"
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    "Package": "maDB",
    "vignettes": [
      "vignettes/maDB/inst/doc/maDB.pdf"
    ],
    "License": "LGPL (>= 2)",
    "biocViews": [
      "Microarray",
      "OneChannel",
      "Software",
      "TwoChannel",
      "Visualization"
    ],
    "Description": "maDB allows to create a simple microarray database to store microarray experiments and annotation data into it. Affymetrix GeneChip expression values as well as values from two color microarrays can be stored into the database. Whole experiments or subsets from a experiment (or also values for a subset of genes in a subset of microarrays) can be fetched back to R. Additionally maDB provides different utility functions for the microarray data analysis like functions to draw MA plots or volcano plots with the data points color coded according to the local point density or functions that allow a replicate handling of miroarrays."
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  "xmapbridge": {
    "Depends": [
      "R (>= 2.0)",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/xmapbridge_1.8.1.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/xmapbridge_1.8.1.tgz",
    "Version": "1.8.1",
    "URL": "http://xmap.picr.man.ac.uk, http://www.bioconductor.org",
    "Maintainer": "Tim Yates <tyates@picr.man.ac.uk>",
    "Author": "Tim Yates <tyates@picr.man.ac.uk> and Crispin J Miller <cmiller@picr.man.ac.uk>",
    "Title": "Export plotting files to the xmapBridge for visualisation in X:Map",
    "source.ver": "src/contrib/xmapbridge_1.8.1.tar.gz",
    "Package": "xmapbridge",
    "vignettes": [
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    "License": "LGPL-3",
    "biocViews": [
      "Annotation",
      "ReportWriting",
      "Software",
      "Visualization"
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    "Description": "xmapBridge can plot graphs in the X:Map genome browser. This package exports plotting files in a suitable format.",
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    "Depends": [
      "methods",
      "annotate (>= 1.21.0)",
      "graph (>= 1.21.0)",
      "Biobase",
      "RBGL (>= 1.17.0)",
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      "hypergraph (>= 1.15.2)",
      "AnnotationDbi"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/RpsiXML_1.10.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/RpsiXML_1.10.0.tgz",
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    "URL": "http://www.bioconductor.org",
    "Maintainer": "Jitao David Zhang <j.zhang@dkfz.de>",
    "Author": "Jitao David Zhang, Stefan Wiemann, Marc Carlson, with contributions from Tony Chiang",
    "Title": "R interface to PSI-MI 2.5 files",
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      "org.Hs.eg.db",
      "org.Mm.eg.db",
      "org.Dm.eg.db",
      "org.Rn.eg.db",
      "org.Sc.sgd.db",
      "hom.Hs.inp.db",
      "hom.Mm.inp.db",
      "hom.Dm.inp.db",
      "hom.Rn.inp.db",
      "hom.Sc.inp.db",
      "Rgraphviz",
      "ppiStats"
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    "Package": "RpsiXML",
    "vignettes": [
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      "vignettes/RpsiXML/inst/doc/RpsiXMLApp.pdf"
    ],
    "License": "LGPL-3",
    "biocViews": [
      "Infrastructure",
      "Proteomics",
      "Software"
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    "Description": "Queries, data structure and interface to visualization of interaction datasets. This package inplements the PSI-MI 2.5 standard and supports up to now 8 databases. Further databases supporting PSI-MI 2.5 standard will be added continuously.",
    "importsMe": [
      "ScISI"
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    "win.binary.ver": "bin/windows/contrib/2.12/RpsiXML_1.10.0.zip"
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      "R (>= 2.6.0)",
      "tools",
      "methods",
      "utils",
      "parody",
      "Biobase",
      "affy",
      "lumi"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/arrayMvout_1.8.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/arrayMvout_1.8.0.tgz",
    "Version": "1.8.0",
    "Maintainer": "V. Carey <stvjc@channing.harvard.edu>",
    "Author": "Z. Gao, A. Asare, R. Wang, V. Carey",
    "Title": "multivariate outlier detection for expression array QA",
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    "Imports": [
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      "mdqc",
      "affyContam"
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    "Suggests": [
      "MAQCsubset",
      "mvoutData",
      "lumiBarnes",
      "affyPLM",
      "affydata",
      "hgu133atagcdf"
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    "Package": "arrayMvout",
    "vignettes": [
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      "vignettes/arrayMvout/inst/doc/arrayMvout-lkadas.pdf",
      "vignettes/arrayMvout/inst/doc/arrayMvout-lkda.pdf",
      "vignettes/arrayMvout/inst/doc/arrayMvout.pdf"
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    "License": "Artistic-2.0",
    "biocViews": [
      "Bioinformatics",
      "Infrastructure",
      "Microarray",
      "QualityControl",
      "Software"
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    "Description": "This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate",
    "win.binary.ver": "bin/windows/contrib/2.12/arrayMvout_1.8.0.zip"
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    "Depends": [
      "graph",
      "multtest"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/gage_2.0.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/gage_2.0.0.tgz",
    "Version": "2.0.0",
    "Maintainer": "Weijun Luo <luo@cshl.edu>",
    "Author": "Weijun Luo",
    "Title": "Generally Applicable Gene-set Enrichment for Pathway Analysis",
    "suggestsMe": [
      "gageData"
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    "source.ver": "src/contrib/gage_2.0.0.tar.gz",
    "Suggests": [
      "gageData",
      "GO.db",
      "GSEABase",
      "KEGG.db",
      "org.Hs.eg.db"
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    "License": "GPL (>=2.0)",
    "biocViews": [
      "Bioinformatics",
      "DataRepresentation",
      "DifferentialExpression",
      "GO",
      "Genetics",
      "Microarray",
      "MultipleComparisons",
      "OneChannel",
      "Pathways",
      "RNAseq",
      "Software",
      "TwoChannel"
    ],
    "Description": "GAGE is a published method for gene set or pathway analysis. In gage package, we provide a series of functions for basic GAGE analysis, result processing and presentation. We have also built pipeline routines for of multiple GAGE analysis on different comparisons or samples, the comparison of parallel analysis results, and even the combined analysis of heterogeneous data from different sources/studies. In addition, we also provide demo microarray data and commonly used gene set data based on KEGG pathways and GO terms. These funtions and data are also useful for gene set analysis using other methods.",
    "win.binary.ver": "bin/windows/contrib/2.12/gage_2.0.0.zip"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/CORREP_1.16.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/CORREP_1.16.0.tgz",
    "Version": "1.16.0",
    "Maintainer": "Dongxiao Zhu <doz@stowers-institute.org>",
    "Author": "Dongxiao Zhu and Youjuan Li",
    "Title": "Multivariate Correlation Estimator and Statistical Inference Procedures.",
    "source.ver": "src/contrib/CORREP_1.16.0.tar.gz",
    "Imports": [
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      "stats"
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    "Suggests": [
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    "Package": "CORREP",
    "vignettes": [
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    "License": "GPL (>= 2)",
    "biocViews": [
      "Bioinformatics",
      "Clustering",
      "GraphsAndNetworks",
      "Microarray",
      "Software"
    ],
    "Description": "Multivariate correlation estimation and statistical inference. See package vignette.",
    "win.binary.ver": "bin/windows/contrib/2.12/CORREP_1.16.0.zip"
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      "R (>= 2.6.0)",
      "Biobase",
      "annotate",
      "methods",
      "graph"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/GSEABase_1.12.2.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/GSEABase_1.12.2.tgz",
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      "HTSanalyzeR",
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    "Maintainer": "Biocore Team c/o BioC user list <bioconductor@stat.math.ethz.ch>",
    "Author": "Martin Morgan, Seth Falcon, Robert Gentleman",
    "Title": "Gene set enrichment data structures and methods",
    "suggestsMe": [
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      "gage",
      "GGtools",
      "GlobalAncova",
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      "GSEAlm",
      "PGSEA"
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    "Imports": [
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      "Biobase",
      "graph",
      "methods",
      "XML"
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    "Suggests": [
      "hgu95av2.db",
      "GO.db",
      "org.Hs.eg.db"
    ],
    "Package": "GSEABase",
    "vignettes": [
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    "License": "Artistic-2.0",
    "biocViews": [
      "Bioinformatics",
      "Infrastructure",
      "Software"
    ],
    "Description": "This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).",
    "importsMe": [
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      "cellHTS2",
      "GGBase",
      "GGtools",
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      "PCpheno",
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    "win.binary.ver": "bin/windows/contrib/2.12/GSEABase_1.12.2.zip"
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      "Biobase (>= 1.4.22)",
      "R (>= 1.9.0)",
      "fibroEset",
      "mda"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/pdmclass_1.22.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/pdmclass_1.22.0.tgz",
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    "Maintainer": "James W. MacDonald <jmacdon@med.umich.edu>",
    "Author": "James W. MacDonald, Debashis Ghosh, based in part on pls code of Mike Denham",
    "Title": "Classification of Microarray Samples using Penalized Discriminant Methods",
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    "License": "Artistic-2.0",
    "biocViews": [
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      "Software"
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    "Description": "This package can be used to classify microarray data using one of three penalized regression methods; partial least squares, principal components regression, or ridge regression.",
    "win.binary.ver": "bin/windows/contrib/2.12/pdmclass_1.22.0.zip"
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      "cosmo"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/cosmoGUI_1.16.0.tgz",
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    "URL": "http://cosmoweb.berkeley.edu/intro.html, http://www.bepress.com/ucbbiostat/paper209/",
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    "Author": "Fabian Gallusser, Oliver Bembom, and Sandrine Dudoit",
    "Title": "GUI for constructing constraint sets used by the cosmo package",
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    "Package": "cosmoGUI",
    "License": "LGPL (>= 2)",
    "biocViews": [
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      "SequenceMatching",
      "Software"
    ],
    "Description": "cosmoGUI allows the user to interactively define constraint sets that can be used by the cosmo package to supervise the search for shared motifs in a set of DNA sequences. The constraints can be either adapted from a set of commonly used templates or defined from scratch.",
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      "R (>= 2.7.0)",
      "affy (>= 1.23.4)",
      "Biobase (>= 2.5.5)",
      "methods"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/ArrayTools_1.10.0.tgz",
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    "Maintainer": "Arthur Li <xueli@coh.org>",
    "Author": "Xiwei Wu, Arthur Li",
    "Title": "geneChip Analysis Package",
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    "Imports": [
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      "Biobase",
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      "methods",
      "stats",
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      "xtable"
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      "hugene10sttranscriptcluster.db"
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    "Package": "ArrayTools",
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    "License": "LGPL (>= 2.0)",
    "biocViews": [
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      "DifferentialExpression",
      "Microarray",
      "OneChannel",
      "Preprocessing",
      "QualityControl",
      "ReportWriting",
      "Software",
      "Statistics",
      "Visualization"
    ],
    "Description": "This package is designed to provide solutions for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays. The package generates comprehensive analysis reports in HTML format. Hyperlinks on the report page will lead to a series of QC plots, processed data, and differentially expressed gene lists. Differentially expressed genes are reported in tabular format with annotations hyperlinked to online biological databases.",
    "win.binary.ver": "bin/windows/contrib/2.12/ArrayTools_1.10.0.zip"
  },
  "MVCClass": {
    "Depends": [
      "R (>= 2.1.0)",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/MVCClass_1.24.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/MVCClass_1.24.0.tgz",
    "Version": "1.24.0",
    "dependsOnMe": [
      "BioMVCClass"
    ],
    "Maintainer": "Elizabeth Whalen <ewhalen@hsph.harvard.edu>",
    "Author": "Elizabeth Whalen",
    "Title": "Model-View-Controller (MVC) Classes",
    "source.ver": "src/contrib/MVCClass_1.24.0.tar.gz",
    "Package": "MVCClass",
    "vignettes": [
      "vignettes/MVCClass/inst/doc/MVCClass.pdf"
    ],
    "License": "LGPL",
    "biocViews": [
      "GraphsAndNetworks",
      "Infrastructure",
      "Software",
      "Visualization"
    ],
    "Description": "Creates classes used in model-view-controller (MVC) design",
    "win.binary.ver": "bin/windows/contrib/2.12/MVCClass_1.24.0.zip"
  },
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    "Depends": [
      "R (>= 2.9.0)",
      "mclust",
      "graphics",
      "grDevices",
      "methods",
      "ShortRead"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/Rolexa_1.6.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/Rolexa_1.6.0.tgz",
    "Version": "1.6.0",
    "Maintainer": "Jacques Rougemont <jacques.rougemont@epfl.ch>",
    "Author": "Jacques Rougemont, Arnaud Amzallag, Christian Iseli, Laurent Farinelli, Ioannis Xenarios, Felix Naef",
    "Title": "Statistical analysis of Solexa sequencing data",
    "source.ver": "src/contrib/Rolexa_1.6.0.tar.gz",
    "Imports": [
      "Biostrings",
      "graphics",
      "grDevices",
      "IRanges",
      "methods",
      "ShortRead",
      "stats"
    ],
    "Package": "Rolexa",
    "vignettes": [
      "vignettes/Rolexa/inst/doc/Rolexa-vignette.pdf"
    ],
    "License": "GPL-2",
    "biocViews": [
      "DataImport",
      "Preprocessing",
      "QualityControl",
      "Sequencing",
      "Software"
    ],
    "Description": "Provides probabilistic base calling, quality checks and diagnostic plots for Solexa sequencing data",
    "Enhances": [
      "fork"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/Rolexa_1.6.0.zip"
  },
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    "Depends": [
      "R (>= 2.0.0)"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/Rdisop_1.10.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/Rdisop_1.10.0.tgz",
    "Version": "1.10.0",
    "URL": "http://msbi.ipb-halle.de/",
    "Maintainer": "Steffen Neumann <sneumann@ipb-halle.de>",
    "Author": "Anton Pervukhin <apervukh@minet.uni-jena.de>, Steffen Neumann <sneumann@ipb-halle.de>",
    "Title": "Decomposition of Isotopic Patterns",
    "source.ver": "src/contrib/Rdisop_1.10.0.tar.gz",
    "Package": "Rdisop",
    "vignettes": [
      "vignettes/Rdisop/inst/doc/Rdisop-isotopes.pdf",
      "vignettes/Rdisop/inst/doc/Rdisop.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL",
    "biocViews": [
      "MassSpectrometry",
      "Software",
      "Technology"
    ],
    "Description": "Identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists.",
    "SystemRequirements": "None",
    "win.binary.ver": "bin/windows/contrib/2.12/Rdisop_1.10.0.zip"
  },
  "RTools4TB": {
    "Depends": [
      "R (>= 2.5.1)",
      "Biobase",
      "limma",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/RTools4TB_1.6.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/RTools4TB_1.6.0.tgz",
    "Version": "1.6.0",
    "URL": "http://tagc.univ-mrs.fr/tbrowser/",
    "Maintainer": "Aurelie Bergon <bergon@tagc.univ-mrs.fr>",
    "Author": "Aurelie Bergon, Fabrice Lopez, Julien Textoris, Samuel Granjeaud and Denis Puthier",
    "Title": "Data mining of public microarray data through connections to the TranscriptomeBrowser database.",
    "source.ver": "src/contrib/RTools4TB_1.6.0.tar.gz",
    "Suggests": [
      "RColorBrewer",
      "biocGraph",
      "ALL"
    ],
    "Package": "RTools4TB",
    "vignettes": [
      "vignettes/RTools4TB/inst/doc/RTools4TB.pdf"
    ],
    "Archs": "i386, x64",
    "License": "LGPL",
    "biocViews": [
      "Annotation",
      "Classification",
      "Clustering",
      "DataImport",
      "GeneExpression",
      "Microarray",
      "OneChannel",
      "Software",
      "TwoChannel"
    ],
    "Description": "TranscriptomeBrowser (TBrowser) hosts a large collection of transcriptional signatures (TS) automatically extracted from the Gene Expression Omnibus (GEO) database. Each GEO experiment (GSE) was processed so that a subset of the original expression matrix containing the most relevant/informative genes was kept and organized into a set of homogeneous signatures. Each signature was tested for functional enrichment using annotations terms obtained from numerous ontologies or curated databases (Gene Ontology, KEGG, BioCarta, Swiss-Prot, BBID, SMART, NIH Genetic Association DB, COG/KOG...) using the DAVID knowledgebase. The RTools4TB package can be used to perform complexe queries to the database. Thereby, RTools4TB can be helpful (i) to define the biological contexts (i.e, experiments) in which a set of genes are co-expressed and (ii) to define their most frequent neighbors. In addition, RTools4TB comes with a new algoritm, \"Density Based Filtering And Markov Clustering\" (DBF-MCL), whose goal is to partition large and noisy datasets. DBF-MCL is a tree-step adaptative algorithm that (i) find elements located in dense areas (ie. clusters) (ii) uses selected items to construct a graph and (iii) performs graph partitioning using MCL. This algorithm is implemented in the RTools4TB package although it requires a UNIX-like systems.",
    "win.binary.ver": "bin/windows/contrib/2.12/RTools4TB_1.6.0.zip"
  },
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    "Depends": [
      "methods",
      "IRanges (>= 1.7.23)",
      "GenomicRanges",
      "Biostrings (>= 2.13.52)",
      "lattice",
      "Rsamtools"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/ShortRead_1.8.2.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/ShortRead_1.8.2.tgz",
    "Version": "1.8.2",
    "dependsOnMe": [
      "chipseq",
      "ChIPseqR",
      "DEGseq",
      "EatonEtAlChIPseq",
      "girafe",
      "OTUbase",
      "Rolexa",
      "segmentSeq"
    ],
    "Maintainer": "Biocore Team c/o BioC user list <bioconductor@stat.math.ethz.ch>",
    "Author": "Martin Morgan, Michael Lawrence, Simon Anders",
    "Title": "Classes and methods for high-throughput short-read sequencing data.",
    "suggestsMe": [
      "CSAR",
      "Genominator",
      "PICS",
      "R453Plus1Toolbox",
      "Rsamtools",
      "yeastRNASeq"
    ],
    "source.ver": "src/contrib/ShortRead_1.8.2.tar.gz",
    "Imports": [
      "IRanges",
      "GenomicRanges",
      "Biostrings",
      "Biobase",
      "hwriter",
      "Rsamtools"
    ],
    "Suggests": [
      "biomaRt",
      "RUnit"
    ],
    "Package": "ShortRead",
    "vignettes": [
      "vignettes/ShortRead/inst/doc/Overview.pdf",
      "vignettes/ShortRead/inst/doc/ShortRead_and_HilbertVis.pdf"
    ],
    "Archs": "i386, x64",
    "License": "Artistic-2.0",
    "LinkingTo": "IRanges, Biostrings",
    "biocViews": [
      "DataImport",
      "HighThroughputSequencing",
      "QualityControl",
      "Sequencing",
      "Software"
    ],
    "Description": "Base classes, functions, and methods for representation of high-throughput, short-read sequencing data.",
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      "Rmpi",
      "multicore"
    ],
    "importsMe": [
      "chipseq",
      "ChIPseqR",
      "ChIPsim",
      "OTUbase",
      "R453Plus1Toolbox",
      "Rolexa"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/ShortRead_1.8.2.zip"
  },
  "mBPCR": {
    "Depends": [
      "oligoClasses",
      "SNPchip"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/mBPCR_1.4.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/mBPCR_1.4.0.tgz",
    "Version": "1.4.0",
    "URL": "http://www.idsia.ch/~paola/mBPCR",
    "Maintainer": "P.M.V. Rancoita <paola@idsia.ch>",
    "Author": "P.M.V. Rancoita <paola@idsia.ch>, with contributions from M. Hutter <marcus.hutter@anu.edu.au>",
    "Title": "Bayesian Piecewise Constant Regression for DNA copy number estimation",
    "source.ver": "src/contrib/mBPCR_1.4.0.tar.gz",
    "Imports": [
      "Biobase"
    ],
    "Suggests": [
      "xtable"
    ],
    "Package": "mBPCR",
    "vignettes": [
      "vignettes/mBPCR/inst/doc/mBPCR.pdf"
    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "Bioinformatics",
      "CopyNumberVariants",
      "Microarray",
      "SNP",
      "Software",
      "aCGH"
    ],
    "Description": "Estimates the DNA copy number profile using mBPCR to detect regions with copy number changes",
    "win.binary.ver": "bin/windows/contrib/2.12/mBPCR_1.4.0.zip"
  },
  "KCsmart": {
    "Depends": [
      "methods",
      "siggenes",
      "multtest"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/KCsmart_2.8.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/KCsmart_2.8.0.tgz",
    "Version": "2.8.0",
    "Maintainer": "Jorma de Ronde <j.d.ronde@nki.nl>",
    "Author": "Jorma de Ronde, Christiaan Klijn, Arno Velds",
    "Title": "Multi sample aCGH analysis package using kernel convolution",
    "source.ver": "src/contrib/KCsmart_2.8.0.tar.gz",
    "Package": "KCsmart",
    "vignettes": [
      "vignettes/KCsmart/inst/doc/KCS.pdf"
    ],
    "License": "GPL-3",
    "biocViews": [
      "DNACopyNumber",
      "Microarray",
      "Software",
      "Visualization",
      "aCGH"
    ],
    "Description": "Multi sample aCGH analysis package using kernel convolution",
    "Enhances": [
      "Biobase",
      "CGHbase"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/KCsmart_2.8.0.zip"
  },
  "qpgraph": {
    "Depends": [
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/qpgraph_1.6.2.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/qpgraph_1.6.2.tgz",
    "Version": "1.6.2",
    "URL": "http://functionalgenomics.upf.edu/qpgraph",
    "Maintainer": "Robert Castelo <robert.castelo@upf.edu>",
    "Author": "R. Castelo and A. Roverato",
    "Title": "Reverse engineering of molecular regulatory networks with qp-graphs",
    "source.ver": "src/contrib/qpgraph_1.6.2.tar.gz",
    "Imports": [
      "methods",
      "annotate",
      "Matrix",
      "graph",
      "Biobase",
      "AnnotationDbi"
    ],
    "Suggests": [
      "Matrix",
      "mvtnorm",
      "graph",
      "genefilter",
      "Category",
      "org.EcK12.eg.db",
      "GOstats"
    ],
    "Package": "qpgraph",
    "vignettes": [
      "vignettes/qpgraph/inst/doc/qpPCCdistbyTF.pdf",
      "vignettes/qpgraph/inst/doc/qpPreRecComparison.pdf",
      "vignettes/qpgraph/inst/doc/qpPreRecComparisonFullRecall.pdf",
      "vignettes/qpgraph/inst/doc/qpTRnet50pctpre.pdf",
      "vignettes/qpgraph/inst/doc/qpTxRegNet.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL (>= 2)",
    "biocViews": [
      "Bioinformatics",
      "GeneExpression",
      "GraphsAndNetworks",
      "Microarray",
      "Pathways",
      "Software",
      "Transcription"
    ],
    "Description": "q-order partial correlation graphs, or qp-graphs for short, are undirected Gaussian graphical Markov models built from q-order partial correlations. They are useful for learning undirected graphical Gaussian Markov models from data sets where the number of random variables p exceeds the available sample size n as, for instance, in the case of microarray data where they can be employed to reverse engineer a molecular regulatory network.",
    "Enhances": [
      "rlecuyer",
      "snow",
      "Rgraphviz"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/qpgraph_1.6.2.zip"
  },
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    "Depends": [
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/biomaRt_2.6.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/biomaRt_2.6.0.tgz",
    "Version": "2.6.0",
    "dependsOnMe": [
      "ChIPpeakAnno",
      "domainsignatures",
      "gene2pathway",
      "GenomeGraphs"
    ],
    "Maintainer": "Steffen Durinck <sdurinck@lbl.gov>",
    "Author": "Steffen Durinck <sdurinck@lbl.gov>, Wolfgang Huber <huber@ebi.ac.uk>",
    "Title": "Interface to BioMart databases (e.g. Ensembl, COSMIC ,Wormbase and Gramene)",
    "suggestsMe": [
      "BiocCaseStudies",
      "ccTutorial",
      "GeneAnswers",
      "GenomicFeatures",
      "Genominator",
      "leeBamViews",
      "maDB",
      "oneChannelGUI",
      "ShortRead",
      "SIM"
    ],
    "source.ver": "src/contrib/biomaRt_2.6.0.tar.gz",
    "Imports": [
      "XML",
      "RCurl"
    ],
    "Suggests": [
      "annotate"
    ],
    "Package": "biomaRt",
    "vignettes": [
      "vignettes/biomaRt/inst/doc/biomaRt.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "Annotation",
      "Software"
    ],
    "Description": "In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (http://www.biomart.org). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt users direct access to a diverse set of data and enable a wide range of powerful online queries from gene annotation to database mining.",
    "importsMe": [
      "affycoretools",
      "ChIPpeakAnno",
      "GenomicFeatures",
      "HTSanalyzeR",
      "R453Plus1Toolbox",
      "RNAither"
    ],
    "win.binary.ver": "bin/windows/contrib/2.12/biomaRt_2.6.0.zip"
  },
  "frmaTools": {
    "Depends": [
      "R (>= 2.10.0)",
      "affyPLM"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/frmaTools_1.2.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/frmaTools_1.2.0.tgz",
    "Version": "1.2.0",
    "URL": "http://bioconductor.org",
    "Maintainer": "Matthew N. McCall <mmccall@jhsph.edu>",
    "Author": "Matthew N. McCall <mmccall@jhsph.ed>, Rafael A. Irizarry <rafa@jhu.edu>",
    "Title": "Frozen RMA Tools",
    "source.ver": "src/contrib/frmaTools_1.2.0.tar.gz",
    "Imports": [
      "Biobase",
      "methods",
      "affy",
      "preprocessCore",
      "stats",
      "utils"
    ],
    "Suggests": [
      "frma",
      "affyPLM",
      "hgu133aprobe",
      "hgu133atagprobe",
      "hgu133plus2probe",
      "hgu133acdf",
      "hgu133atagcdf",
      "hgu133plus2cdf",
      "hgu133afrmavecs",
      "frmaExampleData"
    ],
    "Package": "frmaTools",
    "vignettes": [
      "vignettes/frmaTools/inst/doc/frmaTools.pdf"
    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "Microarray",
      "Preprocessing",
      "Software"
    ],
    "Description": "Tools for advanced use of the frma package.",
    "win.binary.ver": "bin/windows/contrib/2.12/frmaTools_1.2.0.zip"
  },
  "rflowcyt": {
    "Depends": [
      "R (>= 2.3.0)",
      "fields",
      "hexbin",
      "lattice",
      "locfit",
      "methods",
      "prada",
      "rfcdmin (>= 0.9.0)",
      "splancs",
      "stats",
      "survival",
      "xgobi",
      "xtable"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/rflowcyt_1.22.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/rflowcyt_1.22.0.tgz",
    "Version": "1.22.0",
    "Maintainer": "N. LeMeur <nlemeur@fhcrc.org>",
    "Author": "A.J. Rossini, J.Y. Wan, N. LeMeur and Zoe Moodie",
    "Title": "Statistical tools and data structures for analytic flow cytometry",
    "suggestsMe": [
      "prada",
      "rfcdmin"
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    "Imports": [
      "Biobase",
      "KernSmooth",
      "grDevices",
      "graphics",
      "hexbin",
      "lattice",
      "methods",
      "prada",
      "stats",
      "survival",
      "utils"
    ],
    "Package": "rflowcyt",
    "vignettes": [
      "vignettes/rflowcyt/inst/doc/rflowcyt.pdf"
    ],
    "License": "GPL-2",
    "biocViews": [
      "Bioinformatics",
      "CellBasedAssays",
      "Infrastructure",
      "Software"
    ],
    "Description": "Provides basic S4 data structures and routines for analysing flow cytometry data.",
    "win.binary.ver": "bin/windows/contrib/2.12/rflowcyt_1.22.0.zip"
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    "Depends": [
      "R (>= 2.6.0)",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/affyio_1.18.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/affyio_1.18.0.tgz",
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    "dependsOnMe": [
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      "sscore"
    ],
    "Maintainer": "Benjamin Milo Bolstad <bmb@bmbolstad.com>",
    "Author": "Benjamin Milo Bolstad <bmb@bmbolstad.com>",
    "Title": "Tools for parsing Affymetrix data files",
    "suggestsMe": [
      "BufferedMatrixMethods"
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    "source.ver": "src/contrib/affyio_1.18.0.tar.gz",
    "Package": "affyio",
    "Archs": "i386, x64",
    "License": "LGPL (>= 2)",
    "biocViews": [
      "DataImport",
      "Infrastructure",
      "Microarray",
      "Software"
    ],
    "Description": "Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats.",
    "importsMe": [
      "affy",
      "crlmm",
      "gcrma",
      "makePlatformDesign",
      "oligo",
      "oligoClasses"
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    "win.binary.ver": "bin/windows/contrib/2.12/affyio_1.18.0.zip"
  },
  "HilbertVis": {
    "Depends": [
      "R (>= 2.6.0)",
      "grid",
      "lattice"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/HilbertVis_1.8.0.zip",
    "Version": "1.8.0",
    "dependsOnMe": [
      "HilbertVisGUI"
    ],
    "URL": "http://www.ebi.ac.uk/~anders/hilbert",
    "Maintainer": "Simon Anders <anders@fs.tum.de>",
    "Author": "Simon Anders <anders@fs.tum.de>",
    "Title": "Hilbert curve visualization",
    "source.ver": "src/contrib/HilbertVis_1.8.0.tar.gz",
    "Suggests": [
      "EBImage",
      "IRanges"
    ],
    "Package": "HilbertVis",
    "vignettes": [
      "vignettes/HilbertVis/inst/doc/HilbertDisplay_GUI.pdf",
      "vignettes/HilbertVis/inst/doc/HilbertVis.pdf",
      "vignettes/HilbertVis/inst/doc/Rplots.pdf",
      "vignettes/HilbertVis/inst/doc/ThreeChTest.pdf"
    ],
    "Archs": "i386",
    "License": "GPL (>= 3)",
    "biocViews": [
      "Software",
      "Visualization"
    ],
    "Description": "Functions to visualize long vectors of integer data by means of Hilbert curves",
    "importsMe": [
      "ChIPseqR"
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    "win.binary.ver": "bin/windows/contrib/2.12/HilbertVis_1.8.0.zip"
  },
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    "Depends": [
      "affy",
      "Biobase",
      "GO.db",
      "KEGG.db"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/affycoretools_1.22.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/affycoretools_1.22.0.tgz",
    "Version": "1.22.0",
    "Maintainer": "James W. MacDonald <jmacdon@med.umich.edu>",
    "Author": "James W. MacDonald",
    "Title": "Functions useful for those doing repetitive analyses with Affymetrix GeneChips.",
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      "Agi4x44PreProcess",
      "AgiMicroRna"
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    "source.ver": "src/contrib/affycoretools_1.22.0.tar.gz",
    "Imports": [
      "biomaRt",
      "limma",
      "GOstats",
      "annotate",
      "annaffy",
      "genefilter",
      "gcrma",
      "splines",
      "xtable",
      "AnnotationDbi"
    ],
    "Suggests": [
      "affydata",
      "hgfocuscdf",
      "rgl"
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    "Package": "affycoretools",
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      "OneChannel",
      "ReportWriting",
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    "Description": "Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see.",
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      "caTools",
      "bitops"
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    "Maintainer": "Gabor Csardi <Gabor.Csardi@unil.ch>",
    "Author": "Andreas Luscher <andreas.luescher@a3.epfl.ch>",
    "Title": "Visualize biclusters identified in gene expression data",
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    "Imports": [
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      "ALL",
      "hgu95av2.db",
      "biclust",
      "GO.db",
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      "AnnotationDbi",
      "affy"
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    "Package": "ExpressionView",
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      "vignettes/ExpressionView/inst/doc/ExpressionView.ordering.pdf",
      "vignettes/ExpressionView/inst/doc/ExpressionView.tutorial.pdf"
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    "Archs": "i386, x64",
    "License": "GPL (>= 2)",
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      "Classification",
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      "Microarray",
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      "Visualization"
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    "Description": "ExpressionView visualizes possibly overlapping biclusters in a gene expression matrix. It can use the result of the ISA method (eisa package) or the algorithms in the biclust package or others. The viewer itself was developed using Adobe Flex and runs in a flash-enabled web browser.",
    "win.binary.ver": "bin/windows/contrib/2.12/ExpressionView_1.2.0.zip"
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      "methods",
      "tools",
      "stats",
      "genefilter"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/CNTools_1.6.0.zip",
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    "dependsOnMe": [
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    "Maintainer": "J. Zhang <jzhang@jimmy.harvard.edu>",
    "Author": "Jianhua Zhang",
    "Title": "Convert segment data into a region by sample matrix to allow for other high level computational analyses.",
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    "Package": "CNTools",
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    "License": "LGPL",
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    "Description": "This package provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data",
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    "Depends": [
      "R (>= 2.1.0)",
      "akima"
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    "Version": "1.24.0",
    "Maintainer": "Alexander Ploner <Alexander.Ploner@ki.se>",
    "Author": "Yudi Pawitan <Yudi.Pawitan@ki.se> and Alexander Ploner <Alexander.Ploner@ki.se>",
    "Title": "Operating characteristics plus sample size and local fdr for microarray experiments",
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    "Description": "This package allows to characterize the operating characteristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes).",
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    "Maintainer": "Nusrat Rabbee <nrabbee@post.harvard.edu>",
    "Author": "Nusrat Rabbee <nrabbee@post.harvard.edu>, Gary Wong <wongg62@berkeley.edu>",
    "Title": "A Genotype Calling Algorithm for Affymetrix SNP Arrays",
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    "Description": "A classification algorithm, based on a multi-chip, multi-SNP approach for Affymetrix SNP arrays. Using a large training sample where the genotype labels are known, this aglorithm will obtain more accurate classification results on new data. RLMM is based on a robust, linear model and uses the Mahalanobis distance for classification. The chip-to-chip non-biological variation is removed through normalization. This model-based algorithm captures the similarities across genotype groups and probes, as well as thousands other SNPs for accurate classification. NOTE: 100K-Xba only at for now.",
    "SystemRequirements": "Internal files Xba.CQV, Xba.regions (or other regions file)",
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      "R (>= 2.0)",
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    "Maintainer": "Crispin Miller <cmiller@picr.man.ac.uk>",
    "Author": "Affymetrix Inc., Crispin J Miller, PICR",
    "Title": "Implements the Affymetrix PLIER algorithm",
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    "Imports": [
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    "Description": "The PLIER (Probe Logarithmic Error Intensity Estimate) method produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error at the appropriately at low and high signal values.",
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      "R (>= 2.7.0)",
      "tools",
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    "Version": "1.8.0",
    "Maintainer": "V. Carey <stvjc@channing.harvard.edu>",
    "Author": "V. Carey",
    "Title": "structured corruption of affymetrix cel file data",
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    "Package": "affyContam",
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    "License": "Artistic-2.0",
    "biocViews": [
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      "Infrastructure",
      "Software"
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    "Description": "structured corruption of cel file data to demonstrate QA effectiveness",
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      "R (>= 2.11.0)",
      "Biobase",
      "GSEABase"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/PROMISE_1.2.0.zip",
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    "Maintainer": "Xueyuan Cao <xueyuan.cao@stjude.org>",
    "Author": "Stan Pounds <stanley.pounds@stjude.org>, Xueyuan Cao <xueyuan.cao@stjude.org>",
    "Title": "PRojection Onto the Most Interesting Statistical Evidence",
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    "Imports": [
      "Biobase",
      "GSEABase",
      "stats"
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    "Package": "PROMISE",
    "vignettes": [
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    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "Bioinformatics",
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      "MultipleComparisons",
      "OneChannel",
      "Software"
    ],
    "Description": "A general tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables as described in Pounds et. al. (2009) Bioinformatics 25: 2013-2019",
    "win.binary.ver": "bin/windows/contrib/2.12/PROMISE_1.2.0.zip"
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      "R (>= 2.3.0)",
      "methods"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/baySeq_1.4.0.zip",
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      "segmentSeq"
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    "Maintainer": "Thomas J. Hardcastle <tjh48@cam.ac.uk>",
    "Author": "Thomas J. Hardcastle",
    "Title": "Empirical Bayesian analysis of patterns of differential expression in count data",
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    "Suggests": [
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    ],
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    "vignettes": [
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    "License": "GPL-3",
    "biocViews": [
      "Bioinformatics",
      "DifferentialExpression",
      "HighThroughputSequencing",
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      "SAGE",
      "Software"
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    "Description": "This package identifies differential expression in high-throughput 'count' data, such as that derived from next-generation sequencing machines, calculating estimated posterior likelihoods of differential expression (or more complex hypotheses) via empirical Bayesian methods.",
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    "win.binary.ver": "bin/windows/contrib/2.12/baySeq_1.4.0.zip"
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      "survival"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/CGEN_1.2.0.zip",
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    "Version": "1.2.0",
    "Maintainer": "William Wheeler <wheelerb@imsweb.com>",
    "Author": "Samsiddhi Bhattacharjee, Nilanjan Chatterjee and William Wheeler",
    "Title": "An R package for analysis of case-control studies in genetic epidemiology",
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    "Package": "CGEN",
    "vignettes": [
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    ],
    "Archs": "i386, x64",
    "License": "GPL-2",
    "biocViews": [
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      "SNP",
      "Software"
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    "Description": "An R package for analysis of case-control studies in genetic epidemiology",
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  },
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      "rJava (>= 0.4)",
      "graph (>= 1.10.2)",
      "RUnit (>= 0.4.17)"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/gaggle_1.18.0.zip",
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    "Version": "1.18.0",
    "URL": "http://gaggle.systemsbiology.org",
    "Maintainer": "Dan Tenenbaum <dtenenbaum@systemsbiology.org>",
    "Author": "Paul Shannon <pshannon@systemsbiology.org>",
    "Title": "Broadcast data between R and other bioinformatics programs",
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    "Package": "gaggle",
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    "License": "GPL (>= 2)",
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      "Software",
      "Visualization"
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    "Description": "this package contains functions connecting R with the Gaggle",
    "win.binary.ver": "bin/windows/contrib/2.12/gaggle_1.18.0.zip"
  },
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      "tcltk"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/limmaGUI_1.26.0.zip",
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    "URL": "http://bioinf.wehi.edu.au/limmaGUI/",
    "Maintainer": "Keith Satterley <keith@wehi.edu.au>",
    "Author": "James Wettenhall Division of Genetics and Bioinformatics, WEHI",
    "Title": "GUI for limma package",
    "source.ver": "src/contrib/limmaGUI_1.26.0.tar.gz",
    "Suggests": [
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      "xtable",
      "tkrplot"
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    "Package": "limmaGUI",
    "vignettes": [
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      "vignettes/limmaGUI/inst/doc/limmaGUI.pdf",
      "vignettes/limmaGUI/inst/doc/LinModIntro.pdf"
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    "License": "LGPL",
    "biocViews": [
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      "DataImport",
      "DifferentialExpression",
      "GUI",
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      "MultipleComparisons",
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      "TwoChannel"
    ],
    "Description": "A Graphical User Interface for the limma Microarray package",
    "win.binary.ver": "bin/windows/contrib/2.12/limmaGUI_1.26.0.zip"
  },
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      "R (>= 2.10.0)",
      "Biobase (>= 2.5.5)",
      "multtest",
      "survival",
      "affy"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/LMGene_2.6.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/LMGene_2.6.0.tgz",
    "Version": "2.6.0",
    "URL": "http://dmrocke.ucdavis.edu/software.html",
    "Maintainer": "Blythe Durbin-Johnson <bpdurbin@ucdavis.edu>",
    "Author": "David Rocke, Geun Cheol Lee, John Tillinghast, Blythe Durbin-Johnson, and Shiquan Wu",
    "Title": "LMGene Software for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays",
    "source.ver": "src/contrib/LMGene_2.6.0.tar.gz",
    "Suggests": [
      "affydata"
    ],
    "Package": "LMGene",
    "vignettes": [
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    ],
    "License": "LGPL",
    "biocViews": [
      "Bioinformatics",
      "DifferentialExpression",
      "Microarray",
      "Preprocessing",
      "Software"
    ],
    "Description": "LMGene package for analysis of microarray data using a linear model and glog data transformation",
    "win.binary.ver": "bin/windows/contrib/2.12/LMGene_2.6.0.zip"
  },
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      "R (>= 1.7.0)",
      "mclust"
    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/spotSegmentation_1.24.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/spotSegmentation_1.24.0.tgz",
    "Version": "1.24.0",
    "URL": "http://www.stat.washington.edu/fraley",
    "Maintainer": "Chris Fraley <fraley@stat.washington.edu>",
    "Author": "Qunhua Li, Chris Fraley, Adrian Raftery Department of Statistics, University of Washington",
    "Title": "Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots",
    "source.ver": "src/contrib/spotSegmentation_1.24.0.tar.gz",
    "Package": "spotSegmentation",
    "vignettes": [
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    "License": "GPL (>= 2)",
    "biocViews": [
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      "Preprocessing",
      "QualityControl",
      "Software",
      "TwoChannel"
    ],
    "Description": "Spot segmentation via model-based clustering and gridding for blocks within microarray slides, as described in Li et al, Robust Model-Based Segmentation of Microarray Images, Technical Report no. 473, Department of Statistics, University of Washington.",
    "win.binary.ver": "bin/windows/contrib/2.12/spotSegmentation_1.24.0.zip"
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    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/MantelCorr_1.20.0.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/MantelCorr_1.20.0.tgz",
    "Version": "1.20.0",
    "Maintainer": "Brian Steinmeyer <steinmeb@ilya.wustl.edu>",
    "Author": "Brian Steinmeyer and William Shannon",
    "Title": "Compute Mantel Cluster Correlations",
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    "Imports": [
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    ],
    "Package": "MantelCorr",
    "vignettes": [
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    ],
    "License": "GPL (>= 2)",
    "biocViews": [
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      "Clustering",
      "Software"
    ],
    "Description": "Computes Mantel cluster correlations from a (p x n) numeric data matrix (e.g. microarray gene-expression data).",
    "win.binary.ver": "bin/windows/contrib/2.12/MantelCorr_1.20.0.zip"
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      "methods"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/beadarray_2.0.6.zip",
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.12/beadarray_2.0.6.tgz",
    "Version": "2.0.6",
    "Maintainer": "Mark Dunning <Mark.Dunning@cancer.org.uk>",
    "Author": "Mark Dunning, Mike Smith, Jonathan Cairns, Andy Lynch, Matt Ritchie",
    "Title": "Quality assessment and low-level analysis for Illumina BeadArray data",
    "suggestsMe": [
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    "Imports": [
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      "limma"
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    "Suggests": [
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      "affy",
      "hwriter"
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    "Package": "beadarray",
    "vignettes": [
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      "vignettes/beadarray/inst/doc/beadlevel.pdf",
      "vignettes/beadarray/inst/doc/beadsummary.pdf"
    ],
    "Archs": "i386, x64",
    "License": "GPL-2",
    "biocViews": [
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      "Preprocessing",
      "QualityControl",
      "Software"
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    "Description": "The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio.  Methods for quality assessment and low-level analysis are provided.",
    "importsMe": [
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    "win.binary.ver": "bin/windows/contrib/2.12/beadarray_2.0.6.zip"
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    ],
    "win64.binary.ver": "bin/windows64/contrib/2.12/DEDS_1.24.0.zip",
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    "Version": "1.24.0",
    "Maintainer": "Yuanyuan Xiao <yxiao@itsa.ucsf.edu>",
    "Author": "Yuanyuan Xiao <yxiao@itsa.ucsf.edu>, Jean Yee Hwa Yang <jeany@maths.usyd.edu.au>.",
    "Title": "Differential Expression via Distance Summary for Microarray Data",
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    "Package": "DEDS",
    "vignettes": [
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    "Archs": "i386, x64",
    "License": "LGPL",
    "biocViews": [
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      "DifferentialExpression",
      "Microarray",
      "Software"
    ],
    "Description": "This library contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also implements a new methodology called DEDS (Differential Expression via Distance Summary), which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach.",
    "win.binary.ver": "bin/windows/contrib/2.12/DEDS_1.24.0.zip"
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      "rjags(>= 2.1.0)",
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    "URL": "http://www.cancerbiostats.onc.jhmi.edu/cogaps.cfm",
    "Maintainer": "Elana J. Fertig <ejfertig@jhmi.edu>, Michael F. Ochs <mfo@jhu.edu>",
    "Author": "Elana J. Fertig",
    "Title": "Coordinated Gene Activity in Pattern Sets",
    "source.ver": "src/contrib/CoGAPS_1.0.0.tar.gz",
    "Imports": [
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      "grDevices",
      "methods",
      "stats",
      "utils"
    ],
    "Package": "CoGAPS",
    "vignettes": [
      "vignettes/CoGAPS/inst/doc/CoGAPSUsersManual.pdf"
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    "License": "GPL (== 2)",
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    "Description": "Coordinated Gene Activity in Pattern Sets (CoGAPS) infers biological processes which are active in individual gene sets from corresponding microarray measurements.  CoGAPS achieves this inference by combining a MCMC matrix decomposition algorithm (GAPS) with a novel statistic inferring activity on gene sets.",
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    "Author": "Ka Yee Yeung, University of Washington, Seattle, WA, with contributions from Adrian Raftery and Ian Painter",
    "Title": "The Iterative Bayesian Model Averaging (BMA) algorithm",
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    "Author": "Reid F. Thompson <rthompso@aecom.yu.edu>, John M. Greally <jgreally@aecom.yu.edu>",
    "Title": "Analytical Tools for MassArray Data",
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    "Author": "Amalia Annest, University of Washington, Tacoma, WA Ka Yee Yeung, University of Washington, Seattle, WA",
    "Title": "The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis",
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    "Author": "Michael Lawrence, Vince Carey, Robert Gentleman",
    "Title": "R interface to genome browsers and their annotation tracks",
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    "Author": "R. Gentleman and S. Falcon",
    "Title": "Tools for manipulating GO and microarrays.",
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    "Maintainer": "VJ Carey <stvjc@channing.harvard.edu>",
    "Author": "VJ Carey <stvjc@channing.harvard.edu>",
    "Title": "Parametric And Resistant Outlier DYtection",
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    "Package": "parody",
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    "Description": "routines for univariate and multivariate outlier detection with a focus on parametric methods, but support for some methods based on resistant statistics",
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    "Maintainer": "Biocore Team c/o BioC user list <bioconductor@stat.math.ethz.ch>",
    "Author": "P. Aboyoun, H. Pages and M. Lawrence",
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    "Description": "The ability to efficiently store genomic annotations and alignments is playing a central role when it comes to analyze high-throughput sequencing data (a.k.a. NGS data). The package defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome.",
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      "e1071 (>= 1.5)",
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      "time (>= 1.0)",
      "cluster (>= 1.11)"
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    "URL": "http://www.bioconductor.org",
    "Maintainer": "Christian Bender <c.bender@dkfz-heidelberg.de>",
    "Author": "Holger Froehlich, Florian Markowetz, Achim Tresch, Christian Bender, Matthias Maneck, Claudio Lottaz, Tim Beissbarth",
    "Title": "Nested Effects Models to reconstruct phenotypic hierarchies",
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    "Imports": [
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      "graph",
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      "vignettes/nem/inst/doc/nem.pdf"
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    "License": "GPL (>= 2)",
    "biocViews": [
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      "Microarray",
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    "Description": "The package 'nem' allows to reconstruct features of pathways from the nested structure of perturbation effects. It takes as input (1.) a set of pathway components, which were perturbed, and (2.) high-dimensional phenotypic readout of these perturbations (e.g. gene expression or morphological profiles). The output is a directed graph representing the phenotypic hierarchy.",
    "win.binary.ver": "bin/windows/contrib/2.12/nem_2.14.0.zip"
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      "Biobase (>= 2.5.5)"
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    "Author": "Matthew N McCall <mmccall@jhsph.edu>, Rafael A Irizarry <rafa@jhu.edu>",
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    "Imports": [
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    "License": "GPL (>= 2)",
    "biocViews": [
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      "Software"
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    "Description": "The package contains functions that can be used to compare expression measures on different array platforms.",
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      "GLAD",
      "ITALICSData",
      "oligo",
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      "pd.mapping50k.xba240"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/ITALICS_2.10.0.zip",
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    "Maintainer": "Guillem Rigaill <italics@curie.fr>",
    "Author": "Guillem Rigaill, Philippe Hupe",
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    "Imports": [
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    "Package": "ITALICS",
    "vignettes": [
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    "License": "GPL",
    "biocViews": [
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      "Microarray",
      "Software"
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    "Description": "A Method to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set",
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      "Biobase"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/MiChip_1.4.0.zip",
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    "Maintainer": "Jonathon Blake <blake@embl.de>",
    "Author": "Jonathon Blake <blake@embl.de>",
    "Title": "MiChip Parsing and Summarizing Functions",
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    "Imports": [
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    "Package": "MiChip",
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    "biocViews": [
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    ],
    "Description": "This package takes the MiChip miRNA microarray .grp scanner output files and parses these out, providing summary and plotting functions to analyse MiChip hybridizations. A set of hybridizations is packaged into an ExpressionSet allowing it to be used by other BioConductor packages.",
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    "win64.binary.ver": "bin/windows64/contrib/2.12/LPEadj_1.10.0.zip",
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    "Title": "A correction of the local pooled error (LPE) method to replace the asymptotic variance adjustment with an unbiased adjustment based on sample size.",
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    "License": "LGPL",
    "biocViews": [
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    "Description": "Two options are added to the LPE algorithm. The original LPE method sets all variances below the max variance in the ordered distribution of variances to the maximum variance. in LPEadj this option is turned off by default.  The second option is to use a variance adjustment based on sample size rather than pi/2.  By default the LPEadj uses the sample size based variance adjustment.",
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    "Package": "BeadDataPackR",
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    "Description": "Provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform",
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    "Author": "Jean(ZHIJIN) Wu, Rafael Irizarry with contributions from James MacDonald <jmacdon@med.umich.edu> Jeff Gentry",
    "Title": "Background Adjustment Using Sequence Information",
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      "methods",
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    "Author": "Oleg Sklyar, Gregoire Pau, Mike Smith, Wolfgang Huber",
    "Title": "Image processing toolbox for R",
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    "Maintainer": "Laurent Gatto <laurent.gatto@gmail.com>",
    "Author": "Laurent Gatto",
    "Title": "Affymetrix expression data quality control and reproducibility analysis",
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      "methods",
      "isa2",
      "Biobase",
      "AnnotationDbi",
      "Category",
      "genefilter",
      "DBI"
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    "Maintainer": "Gabor Csardi <Gabor.Csardi@unil.ch>",
    "Author": "Gabor Csardi <Gabor.Csardi@unil.ch>",
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    "License": "GPL (>= 2)",
    "biocViews": [
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    ],
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    "win64.binary.ver": "bin/windows64/contrib/2.12/aroma.light_1.18.4.zip",
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    "URL": "http://www.aroma-project.org/",
    "Maintainer": "Henrik Bengtsson <henrikb@braju.com>",
    "Author": "Henrik Bengtsson <henrikb@braju.com>",
    "Title": "Light-weight methods for normalization and visualization of microarray data using only basic R data types",
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    "Package": "aroma.light",
    "License": "LGPL (>= 2.1)",
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      "MultiChannel",
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      "Visualization"
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    "Description": "Methods for microarray analysis that take basic data types such as matrices and lists of vectors.  These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes.",
    "win.binary.ver": "bin/windows/contrib/2.12/aroma.light_1.18.4.zip"
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      "topGO",
      "RankProd",
      "prada"
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    "win64.binary.ver": "bin/windows64/contrib/2.12/RNAither_1.10.0.zip",
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    "Author": "Nora Rieber and Lars Kaderali, University of Heidelberg, Viroquant Research Group Modeling, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany",
    "Title": "Statistical analysis of high-throughput RNAi screens",
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    "License": "Artistic-2.0",
    "biocViews": [
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      "CellBasedAssays",
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      "Visualization"
    ],
    "Description": "RNAither analyzes cell-based RNAi screens, and includes quality assessment, customizable normalization and statistical tests, leading to lists of significant genes and biological processes.",
    "win.binary.ver": "bin/windows/contrib/2.12/RNAither_1.10.0.zip"
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}