{
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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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    "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.",
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    "win.binary.ver": "bin/windows/contrib/2.10/TypeInfo_1.12.0.zip"
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      "limma",
      "tilingArray",
      "DNAcopy",
      "GLAD",
      "cluster",
      "methods",
      "aCGH"
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    "Version": "1.16.0",
    "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.",
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    "License": "GPL",
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      "Microarray",
      "Preprocessing",
      "Software",
      "TwoChannel"
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    "Description": "Methods for segmenting, normalising and processing aCGH data; including plotting functions for visualising raw and segmented data for individual and multiple arrays.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/snapCGH_1.16.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/snapCGH_1.16.0.zip"
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      "limma",
      "methods"
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    "URL": "http://tagc.univ-mrs.fr/tbrowser/",
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    "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.",
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    "win.binary.ver": "bin/windows/contrib/2.10/RTools4TB_1.2.0.zip"
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      "methods",
      "stats",
      "locfit",
      "Biobase",
      "marray"
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    "Maintainer": "Matthias Futschik <mfutschik@ualg.pt>",
    "Author": "Matthias Futschik <mfutschik@ualg.pt>",
    "Title": "Optimized local intensity-dependent normalisation of two-color microarrays",
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    "Package": "OLIN",
    "vignettes": [
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    "License": "GPL-2",
    "biocViews": [
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      "Preprocessing",
      "QualityControl",
      "Software",
      "TwoChannel",
      "Visualization"
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    "Description": "Functions for normalisation of two-color microarrays by optimised local regression and for detection of artefacts in microarray data",
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    "win.binary.ver": "bin/windows/contrib/2.10/OLIN_1.24.0.zip"
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      "RColorBrewer",
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    "Maintainer": "Vince Carey <stvjc@channing.harvard.edu>",
    "Author": "Vince Carey <stvjc@channing.harvard.edu>",
    "Title": "software and data for genetical genomics (c) 2006 VJ Carey",
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      "org.Hs.eg.db",
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    "Package": "GGtools",
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      "vignettes/GGtools/inst/doc/GGoverview2008.pdf"
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    "License": "Artistic-2.0",
    "biocViews": [
      "Bioinformatics",
      "GeneticVariability",
      "Genetics",
      "SNP",
      "Software"
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    "Description": "dealing with hapmap SNP reports, GWAS, etc.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/GGtools_3.4.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/GGtools_3.4.0.zip"
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    "Depends": [
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    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/CNVtools_1.40.2.tgz",
    "Version": "1.40.2",
    "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",
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    "Package": "CNVtools",
    "vignettes": [
      "vignettes/CNVtools/inst/doc/CNVtools-vignette.pdf"
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    "License": "GPL-3",
    "biocViews": [
      "DNACopyNumber",
      "GeneticVariability",
      "Software"
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    "Description": "This package is meant to facilitate the testing of Copy Number Variant data for genetic association, typically in case-control studies.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/CNVtools_1.40.2.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/CNVtools_1.40.2.zip"
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  "GEOquery": {
    "Depends": [
      "methods",
      "Biobase",
      "RCurl"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/GEOquery_2.11.3.tgz",
    "Version": "2.11.3",
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    "URL": "http://watson.nci.nih.gov/~sdavis",
    "Maintainer": "Sean Davis <sdavis2@mail.nih.gov>",
    "Author": "Sean Davis <sdavis2@mail.nih.gov>",
    "Title": "Get data from NCBI Gene Expression Omnibus (GEO)",
    "suggestsMe": [
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    "Package": "GEOquery",
    "vignettes": [
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    "License": "GPL-2",
    "biocViews": [
      "DataImport",
      "Microarray",
      "OneChannel",
      "SAGE",
      "Software",
      "TwoChannel"
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    "Description": "The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data.  Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data.  GEOquery is the bridge between GEO and BioConductor.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/GEOquery_2.11.3.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/GEOquery_2.11.3.zip"
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      "R (>= 1.8.0)",
      "Biobase",
      "utils",
      "lattice",
      "cluster",
      "methods"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/EBarrays_2.10.0.tgz",
    "Version": "2.10.0",
    "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": [
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    "Package": "EBarrays",
    "vignettes": [
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    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "Software"
    ],
    "Description": "EBarrays provides tools for the analysis of replicated/unreplicated microarray data.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/EBarrays_2.10.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/EBarrays_2.10.0.zip"
  },
  "SNPchip": {
    "Depends": [
      "R (>= 2.6.0)",
      "Biobase (>= 2.5.5)",
      "methods",
      "oligoClasses (>= 1.7.8)",
      "graphics"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/SNPchip_1.10.0.tgz",
    "Version": "1.10.0",
    "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"
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    "source.ver": "src/contrib/SNPchip_1.10.0.tar.gz",
    "Imports": [
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      "graphics",
      "grDevices",
      "methods",
      "oligoClasses (>= 1.7.8)",
      "stats",
      "utils"
    ],
    "Suggests": [
      "RSQLite",
      "VanillaICE",
      "RColorBrewer",
      "genefilter",
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    "Package": "SNPchip",
    "vignettes": [
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      "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.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/SNPchip_1.10.0.tgz",
    "importsMe": [
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      "VanillaICE"
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    "win.binary.ver": "bin/windows/contrib/2.10/SNPchip_1.10.0.zip"
  },
  "GGBase": {
    "Depends": [
      "R (>= 2.7.0)",
      "methods",
      "Biobase (>= 2.5.5)",
      "GSEABase",
      "snpMatrix(>= 1.7.6)",
      "RSQLite"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/GGBase_3.6.0.tgz",
    "Version": "3.6.0",
    "dependsOnMe": [
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      "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": [
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    "Imports": [
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      "illuminaHumanv1.db"
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    "Package": "GGBase",
    "vignettes": [
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      "vignettes/GGBase/inst/doc/makeSMLset.pdf",
      "vignettes/GGBase/inst/doc/newSNPloc.pdf"
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    "License": "Artistic-2.0",
    "biocViews": [
      "Bioinformatics",
      "GeneticVariability",
      "Genetics",
      "SNP",
      "Software"
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    "Description": "infrastructure for dealing with hapmap SNP reports, GWAS, etc.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/GGBase_3.6.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/GGBase_3.6.0.zip"
  },
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      "R (>= 2.6.0)",
      "affy (>= 1.11.0)",
      "Biobase",
      "methods",
      "gcrma",
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      "preprocessCore (>= 1.5.1)"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/affyPLM_1.22.0.tgz",
    "Version": "1.22.0",
    "dependsOnMe": [
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      "arrayQualityMetrics",
      "RefPlus"
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    "URL": "http://bmbolstad.com",
    "Maintainer": "Ben Bolstad <bmb@bmbolstad.com>",
    "Author": "Ben Bolstad <bmb@bmbolstad.com>",
    "Title": "Methods for fitting probe-level models",
    "suggestsMe": [
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    "Suggests": [
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      "vignettes/affyPLM/inst/doc/MAplots.pdf",
      "vignettes/affyPLM/inst/doc/QualityAssess.pdf",
      "vignettes/affyPLM/inst/doc/ThreeStep.pdf"
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    "License": "GPL (>= 2)",
    "LinkingTo": "preprocessCore",
    "biocViews": [
      "Microarray",
      "OneChannel",
      "Preprocessing",
      "QualityControl",
      "Software"
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    "Description": "A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/affyPLM_1.22.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/affyPLM_1.22.0.zip"
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      "Biobase (>= 2.4.0)"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/ArrayExpress_1.6.2.tgz",
    "Version": "1.6.2",
    "Maintainer": "Audrey Kauffmann <audrey@ebi.ac.uk>",
    "Author": "Audrey Kauffmann",
    "Title": "Access the ArrayExpress Microarray Database at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet",
    "source.ver": "src/contrib/ArrayExpress_1.6.2.tar.gz",
    "Imports": [
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      "affy",
      "limma"
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    "Package": "ArrayExpress",
    "vignettes": [
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    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "DataImport",
      "Microarray",
      "OneChannel",
      "Software",
      "TwoChannel"
    ],
    "Description": "Access the ArrayExpress Repository at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/ArrayExpress_1.6.2.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/ArrayExpress_1.6.2.zip"
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      "Biobase (>= 2.5.5)",
      "methods"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/beadarray_1.14.0.tgz",
    "Version": "1.14.0",
    "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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      "lumi"
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    "Imports": [
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      "limma"
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      "affy"
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      "vignettes/beadarray/inst/doc/beadarray.pdf",
      "vignettes/beadarray/inst/doc/beadlevel.pdf",
      "vignettes/beadarray/inst/doc/beadsummary.pdf"
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    "License": "GPL",
    "biocViews": [
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      "OneChannel",
      "Preprocessing",
      "QualityControl",
      "Software"
    ],
    "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.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/beadarray_1.14.0.tgz",
    "importsMe": [
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    "win.binary.ver": "bin/windows/contrib/2.10/beadarray_1.14.0.zip"
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      "rama"
    ],
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    "Version": "1.10.0",
    "Maintainer": "Raphael Gottardo <raph@stat.ubc.ca>",
    "Author": "Raphael Gottardo",
    "Title": "Bayesian Robust Inference for Differential Gene Expression",
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    "Package": "bridge",
    "vignettes": [
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    "License": "GPL (>= 2)",
    "biocViews": [
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      "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.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/bridge_1.10.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/bridge_1.10.0.zip"
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      "limma",
      "statmod",
      "scatterplot3d",
      "graphics",
      "grDevices",
      "stats",
      "utils",
      "Biobase",
      "tools",
      "methods"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/clippda_1.0.0.tgz",
    "Version": "1.0.0",
    "URL": "http://www.cancerstudies.bham.ac.uk/crctu/CLIPPDA.shtml",
    "Maintainer": "Stephen Nyangoma <s.o.nyangoma@bham.ac.uk>",
    "Author": "Stephen Nyangoma",
    "Title": "A package for the clinical proteomic profiling data analysis",
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      "DataPreprocessing",
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    ],
    "Description": "Methods for the nalysis of data from clinical proteomic profiling studies. The focus is on the studies of human subjects, which are often observational case-control by design and have technical replicates. A method for sample size determination for planning these studies is proposed. It incorporates routines for adjusting for the expected heterogeneities and imbalances in the data and the within-sample replicate correlations.",
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      "RefPlus",
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      "Ringo",
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    "Maintainer": "Biocore Team c/o BioC user list <bioconductor@stat.math.ethz.ch>",
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    "Description": "Functions that are needed by many other packages or which replace R functions.",
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    ],
    "win.binary.ver": "bin/windows/contrib/2.10/Biobase_2.6.1.zip"
  },
  "TargetSearch": {
    "Depends": [
      "R (>= 2.7.0)",
      "xcms",
      "methods",
      "tcltk"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/TargetSearch_1.2.0.tgz",
    "Version": "1.2.0",
    "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 <hannah@mpimp-golm.mpg.de>",
    "Title": "A package for the analysis of GC-MS metabolite profiling data.",
    "source.ver": "src/contrib/TargetSearch_1.2.0.tar.gz",
    "Imports": [
      "methods"
    ],
    "Suggests": [
      "TargetSearchData"
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    "Package": "TargetSearch",
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    "License": "GPL (>= 2)",
    "biocViews": [
      "MassSpectrometry",
      "Preprocessing",
      "Software",
      "Technology"
    ],
    "Description": "This packages provides a targeted pre-processing method for GC-MS data.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/TargetSearch_1.2.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/TargetSearch_1.2.0.zip"
  },
  "SIM": {
    "Depends": [
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      "quantreg"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/SIM_1.14.0.tgz",
    "Version": "1.14.0",
    "Maintainer": "Maarten van Iterson <M.van_iterson.HG@lumc.nl>",
    "Author": "Renee X. de Menezes and Judith M. Boer",
    "Title": "Integrated Analysis on two human genomic datasets",
    "source.ver": "src/contrib/SIM_1.14.0.tar.gz",
    "Imports": [
      "graphics",
      "stats",
      "globaltest",
      "quantsmooth"
    ],
    "Suggests": [
      "biomaRt",
      "RMySQL"
    ],
    "Package": "SIM",
    "vignettes": [
      "vignettes/SIM/inst/doc/SIM.pdf"
    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "Bioinformatics",
      "DNACopyNumber",
      "Microarray",
      "Software",
      "Visualization"
    ],
    "Description": "Finds associations between two human genomic datasets.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/SIM_1.14.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/SIM_1.14.0.zip"
  },
  "MCRestimate": {
    "Depends": [
      "R (>= 2.7.2)",
      "e1071 (>= 1.5-12)",
      "pamr (>= 1.22)",
      "randomForest (>= 3.9-6)",
      "RColorBrewer (>= 0.1-3)",
      "Biobase (>= 2.5.5)",
      "golubEsets (>= 1.4.6)"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/MCRestimate_2.2.0.tgz",
    "Version": "2.2.0",
    "Maintainer": "Marc Johannes <m.johannes@dkfz.de>",
    "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_2.2.0.tar.gz",
    "Suggests": [
      "xtable (>= 1.2-1)",
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    "Package": "MCRestimate",
    "vignettes": [
      "vignettes/MCRestimate/inst/doc/UsingMCRestimate.pdf"
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    "License": "GPL (>= 2)",
    "biocViews": [
      "Bioinformatics",
      "Classification",
      "Software"
    ],
    "Description": "This package includes a function for combining preprocessing and classification methods to calculate misclassification errors",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/MCRestimate_2.2.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/MCRestimate_2.2.0.zip"
  },
  "affxparser": {
    "Depends": [
      "R (>= 2.6.0)"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/affxparser_1.18.0.tgz",
    "Version": "1.18.0",
    "dependsOnMe": [
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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_1.18.0.tar.gz",
    "Suggests": [
      "R.utils",
      "AffymetrixDataTestFiles"
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    "Package": "affxparser",
    "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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    "importsMe": [
      "GeneRegionScan",
      "oligo",
      "rMAT"
    ],
    "win.binary.ver": "bin/windows/contrib/2.10/affxparser_1.18.0.zip"
  },
  "affyQCReport": {
    "Depends": [
      "Biobase (>= 1.13.16)",
      "affy",
      "simpleaffy",
      "xtable",
      "affyPLM",
      "RColorBrewer",
      "genefilter",
      "lattice"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/affyQCReport_1.24.0.tgz",
    "Version": "1.24.0",
    "Maintainer": "Craig Parman <craig.parman@bifx.org>",
    "Author": "Craig Parman <craig.parman@bifx.org>, Conrad Halling <conrad.halling@bifx.org>, Robert Gentleman",
    "Title": "QC Report Generation for affyBatch objects",
    "suggestsMe": [
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    ],
    "source.ver": "src/contrib/affyQCReport_1.24.0.tar.gz",
    "Suggests": [
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    "Package": "affyQCReport",
    "vignettes": [
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    ],
    "License": "LGPL (>= 2)",
    "biocViews": [
      "Microarray",
      "OneChannel",
      "QualityControl",
      "Software"
    ],
    "Description": "This package creates a QC report for an AffyBatch object. The report is intended to allow the user to quickly assess the quality of a set of arrays in an AffyBatch object.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/affyQCReport_1.24.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/affyQCReport_1.24.0.zip"
  },
  "MiPP": {
    "Depends": [
      "R (>= 2.4)",
      "Biobase",
      "e1071",
      "MASS"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/MiPP_1.18.0.tgz",
    "Version": "1.18.0",
    "URL": "http://www.healthsystem.virginia.edu/internet/hes/biostat/bioinformatics/",
    "Maintainer": "Sukwoo Kim <s4kim@korea.ac.kr>",
    "Author": "HyungJun Cho <hj4cho@korea.ac.kr>, Sukwoo Kim <s4kim@korea.ac.kr>, Mat Soukup <soukup@fda.gov>, and Jae K. Lee <jaeklee@virginia.edu>",
    "Title": "Misclassification Penalized Posterior Classification",
    "source.ver": "src/contrib/MiPP_1.18.0.tar.gz",
    "Package": "MiPP",
    "vignettes": [
      "vignettes/MiPP/inst/doc/MiPP.pdf"
    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "Classification",
      "Microarray",
      "Software"
    ],
    "Description": "This package finds optimal sets of genes that seperate samples into two or more classes.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/MiPP_1.18.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/MiPP_1.18.0.zip"
  },
  "BicARE": {
    "Depends": [
      "R (>= 1.8.0)",
      "Biobase (>= 2.5.5)",
      "multtest",
      "GSEABase"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/BicARE_1.4.0.tgz",
    "Version": "1.4.0",
    "URL": "http://bioinfo.curie.fr",
    "Maintainer": "Pierre Gestraud <pierre.gestraud@curie.fr>",
    "Author": "Pierre Gestraud",
    "Title": "Biclustering Analysis and Results Exploration",
    "source.ver": "src/contrib/BicARE_1.4.0.tar.gz",
    "Package": "BicARE",
    "vignettes": [
      "vignettes/BicARE/inst/doc/BicARE.pdf"
    ],
    "License": "GPL",
    "biocViews": [
      "Bioinformatics",
      "Clustering",
      "Microarray",
      "Software",
      "Transcription"
    ],
    "Description": "Biclustering Analysis and Results Exploration",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/BicARE_1.4.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/BicARE_1.4.0.zip"
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  "tspair": {
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      "Biobase (>= 2.5.5)",
      "time"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/tspair_1.4.0.tgz",
    "Version": "1.4.0",
    "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_1.4.0.tar.gz",
    "Package": "tspair",
    "vignettes": [
      "vignettes/tspair/inst/doc/tsp.pdf",
      "vignettes/tspair/inst/doc/tsp1.pdf"
    ],
    "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.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/tspair_1.4.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/tspair_1.4.0.zip"
  },
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      "affy",
      "affxparser"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/Starr_1.2.11.tgz",
    "Version": "1.2.11",
    "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",
    "source.ver": "src/contrib/Starr_1.2.11.tar.gz",
    "Imports": [
      "pspline",
      "MASS"
    ],
    "Package": "Starr",
    "vignettes": [
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    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "ChIPchip",
      "DataImport",
      "Microarray",
      "OneChannel",
      "Preprocessing",
      "QualityControl",
      "Software"
    ],
    "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.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/Starr_1.2.11.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/Starr_1.2.11.zip"
  },
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      "xtable"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/ssize_1.20.0.tgz",
    "Version": "1.20.0",
    "Maintainer": "Gregory R. Warnes <greg@random-technologies-llc.com>",
    "Author": "Gregory R. Warnes, Peng Liu, and Fasheng Li",
    "Title": "Estimate Microarray Sample Size",
    "suggestsMe": [
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    ],
    "source.ver": "src/contrib/ssize_1.20.0.tar.gz",
    "Package": "ssize",
    "vignettes": [
      "vignettes/ssize/inst/doc/ssize.pdf"
    ],
    "License": "LGPL",
    "biocViews": [
      "Bioinformatics",
      "DifferentialExpression",
      "Microarray",
      "Software"
    ],
    "Description": "Functions for computing and displaying sample size information for gene expression arrays.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/ssize_1.20.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/ssize_1.20.0.zip"
  },
  "rbsurv": {
    "Depends": [
      "R (>= 2.5.0)",
      "Biobase (>= 2.5.5)",
      "survival"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/rbsurv_2.4.0.tgz",
    "Version": "2.4.0",
    "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",
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    "Author": "James W. MacDonald",
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    "Description": "An interactive tool to visualize long vectors of integer data by means of Hilbert curves",
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    "Maintainer": "Hui Zhao <hui.zhao@biw.kuleuven.be>",
    "Author": "Hui Zhao, Kristof Engelen, Bart De Moor and Kathleen Marchal",
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      "Software"
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    "Description": "A package for processing protein mass spectrometry data.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/PROcess_1.22.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/PROcess_1.22.0.zip"
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  "BufferedMatrix": {
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      "R (>= 2.6.0)",
      "methods"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/BufferedMatrix_1.10.0.tgz",
    "Version": "1.10.0",
    "dependsOnMe": [
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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_1.10.0.tar.gz",
    "Package": "BufferedMatrix",
    "vignettes": [
      "vignettes/BufferedMatrix/inst/doc/BufferedMatrix.pdf",
      "vignettes/BufferedMatrix/inst/doc/BufferedMatrixPicture1.pdf",
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      "vignettes/BufferedMatrix/inst/doc/BufferedMatrixPicture3.pdf",
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    "License": "LGPL (>= 2)",
    "biocViews": [
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      "Software"
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    "Description": "A tabular style data object where most data is stored outside main memory. A buffer is used to speed up access to data.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/BufferedMatrix_1.10.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/BufferedMatrix_1.10.0.zip"
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    "Depends": [
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/metahdep_1.4.0.tgz",
    "Version": "1.4.0",
    "Maintainer": "John R. Stevens <john.r.stevens@usu.edu>",
    "Author": "John R. Stevens, Gabriel Nicholas",
    "Title": "Hierarchical Dependence in Meta-Analysis",
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    "Suggests": [
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    "License": "GPL-3",
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      "DifferentialExpression",
      "Microarray",
      "Software"
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    "Description": "Tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/metahdep_1.4.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/metahdep_1.4.0.zip"
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      "R (>= 2.6.0)",
      "Biobase (>= 2.5.5)",
      "affy (>= 1.23.4)",
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      "methods"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/maDB_1.18.0.tgz",
    "Version": "1.18.0",
    "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.",
    "source.ver": "src/contrib/maDB_1.18.0.tar.gz",
    "Suggests": [
      "annaffy (>= 1.6.2)",
      "biomaRt (>= 1.8.2)",
      "geneplotter"
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    "Package": "maDB",
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    ],
    "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.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/maDB_1.18.0.tgz"
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      "R (>= 2.3.0)"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/multiscan_1.6.0.tgz",
    "Version": "1.6.0",
    "Maintainer": "Mizanur Khondoker <mizanur.khondoker@ed.ac.uk>",
    "Author": "Mizanur Khondoker <mizanur.khondoker@ed.ac.uk>, Chris Glasbey, Bruce Worton.",
    "Title": "R package for combining multiple scans",
    "source.ver": "src/contrib/multiscan_1.6.0.tar.gz",
    "Imports": [
      "Biobase",
      "utils"
    ],
    "Package": "multiscan",
    "vignettes": [
      "vignettes/multiscan/inst/doc/multiscan.pdf"
    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "Microarray",
      "Preprocessing",
      "Software"
    ],
    "Description": "Estimates gene expressions from several laser scans of the same microarray",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/multiscan_1.6.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/multiscan_1.6.0.zip"
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    "Version": "1.8.0",
    "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",
    "vignettes": [
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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",
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      "vignettes/GraphAlignment/inst/doc/GraphAlignment.pdf"
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    "License": "file LICENSE",
    "biocViews": [
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      "Software"
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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))",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/GraphAlignment_1.8.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/GraphAlignment_1.8.0.zip"
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    "Depends": [
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      "stats",
      "genefilter"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/CNTools_1.2.0.tgz",
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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.",
    "source.ver": "src/contrib/CNTools_1.2.0.tar.gz",
    "Package": "CNTools",
    "vignettes": [
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    ],
    "License": "LGPL",
    "biocViews": [
      "Microarray",
      "Platform",
      "Software"
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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",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/CNTools_1.2.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/CNTools_1.2.0.zip"
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      "affy (>= 1.23.4)",
      "Biobase (>= 2.5.5)",
      "methods"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/ArrayTools_1.6.0.tgz",
    "Version": "1.6.0",
    "Maintainer": "Arthur Li <xueli@coh.org>",
    "Author": "Xiwei Wu, Arthur Li",
    "Title": "geneChip Analysis Package",
    "source.ver": "src/contrib/ArrayTools_1.6.0.tar.gz",
    "Imports": [
      "affy",
      "Biobase",
      "graphics",
      "grDevices",
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      "methods",
      "stats",
      "utils",
      "xtable"
    ],
    "Suggests": [
      "simpleaffy",
      "R2HTML",
      "affydata",
      "affyPLM",
      "genefilter",
      "annaffy",
      "gcrma",
      "hugene10sttranscriptcluster.db"
    ],
    "Package": "ArrayTools",
    "vignettes": [
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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.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/ArrayTools_1.6.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/ArrayTools_1.6.0.zip"
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  "aCGH": {
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      "R (>= 1.8.0)",
      "cluster",
      "survival",
      "multtest"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/aCGH_1.22.0.tgz",
    "Version": "1.22.0",
    "dependsOnMe": [
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    "Maintainer": "Peter Dimitrov <dimitrov@stat.Berkeley.EDU>",
    "Author": "Jane Fridlyand <jfridlyand@cc.ucsf.edu>, Peter Dimitrov <dimitrov@stat.Berkeley.EDU>",
    "Title": "Classes and functions for Array Comparative Genomic Hybridization data.",
    "suggestsMe": [
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    ],
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    "Imports": [
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      "cluster",
      "grDevices",
      "graphics",
      "methods",
      "multtest",
      "stats",
      "survival",
      "splines",
      "utils"
    ],
    "Package": "aCGH",
    "vignettes": [
      "vignettes/aCGH/inst/doc/aCGH.pdf"
    ],
    "License": "GPL",
    "biocViews": [
      "CopyNumberVariants",
      "DataImport",
      "Genetics",
      "Software"
    ],
    "Description": "Functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/aCGH_1.22.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/aCGH_1.22.0.zip"
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  "tilingArray": {
    "Depends": [
      "Biobase",
      "methods",
      "pixmap"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/tilingArray_1.24.0.tgz",
    "Version": "1.24.0",
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      "snapCGH"
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    "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_1.24.0.tar.gz",
    "Imports": [
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      "affy",
      "vsn",
      "genefilter",
      "RColorBrewer",
      "grid"
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    "Package": "tilingArray",
    "vignettes": [
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      "vignettes/tilingArray/inst/doc/costMatrix.pdf",
      "vignettes/tilingArray/inst/doc/findsegments.pdf",
      "vignettes/tilingArray/inst/doc/segmentation.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "Microarray",
      "OneChannel",
      "Preprocessing",
      "Software",
      "Visualization"
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    "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.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/tilingArray_1.24.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/tilingArray_1.24.0.zip"
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  "DAVIDQuery": {
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    "Version": "1.4.0",
    "Maintainer": "Roger Day <day@upci.pitt.edu>",
    "Author": "Roger Day",
    "Title": "Retrieval from the DAVID bioinformatics data resource into R",
    "source.ver": "src/contrib/DAVIDQuery_1.4.0.tar.gz",
    "Imports": [
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      "utils"
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    "Package": "DAVIDQuery",
    "vignettes": [
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    "License": "GPL-2",
    "biocViews": [
      "AnnotationData",
      "Genomics",
      "Software"
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    "Description": "Tools to retrieve data from DAVID, the Database for Annotation, Visualization and Integrated Discovery",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/DAVIDQuery_1.4.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/DAVIDQuery_1.4.0.zip"
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  "hexbin": {
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      "R (>= 2.0.1)",
      "methods",
      "stats",
      "grid",
      "lattice"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/hexbin_1.20.0.tgz",
    "Version": "1.20.0",
    "dependsOnMe": [
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      "rflowcyt"
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    "Maintainer": "Nicholas Lewin-Koh <nikko@hailmail.net>",
    "Author": "Dan Carr <dcarr@voxel.galaxy.gmu.edu>, ported by Nicholas Lewin-Koh and Martin Maechler <maechler@stat.math.ethz.ch>",
    "Title": "Hexagonal Binning Routines",
    "suggestsMe": [
      "snpMatrix"
    ],
    "source.ver": "src/contrib/hexbin_1.20.0.tar.gz",
    "Suggests": [
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      "cluster",
      "affy",
      "Biobase"
    ],
    "Package": "hexbin",
    "vignettes": [
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    ],
    "License": "GPL-2",
    "biocViews": [
      "Software"
    ],
    "Description": "Binning and plotting functions for hexagonal bins. Now uses and relies on grid graphics and formal (S4) classes and methods.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/hexbin_1.20.0.tgz",
    "importsMe": [
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    "win.binary.ver": "bin/windows/contrib/2.10/hexbin_1.20.0.zip"
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  "fbat": {
    "Depends": [
      "MASS",
      "GeneticsBase"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/fbat_1.10.0.tgz",
    "Version": "1.10.0",
    "Maintainer": "The R Genetics Project <r-genetics-talk@lists.sourceforge.net>",
    "Author": "Weiliang Qiu <stwxq@channing.harvard.edu> Ross Lazarus <ross.lazarus@channing.harvard.edu> Gregory Warnes <warnes@bst.rochester.edu> Nitin Jain <nitin.jain@pfizer.com>",
    "Title": "Family Based Association Tests for genetic data.",
    "source.ver": "src/contrib/fbat_1.10.0.tar.gz",
    "Package": "fbat",
    "vignettes": [
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    ],
    "License": "LGPL",
    "biocViews": [
      "Genetics",
      "Software"
    ],
    "Description": "This package implements a broad class of Family Based Association Tests for genetids data, with adjustments for population admixture using the code from the 'FBAT' software program (see http://www.biostat.harvard.edu/~fbat/fbat.htm). Features include: - Uses data from nuclear families, sibships, pedigrees, or any combination; provides unbiased tests with or without founder genotypes. - Analyzes dichotomous, measured, or time-to-onset traits and multiple traits; trait definition can be optimized. - Offers bi-allelic and multi-allelic tests of association using standard genetic models (additive, dominant, recessive or genotype). - Offers large sample and Monte-Carlo exact tests of the null hypothesis: no linkage and no association; offers large sample test of H0: no association. - Estimates allele frequencies; checks Mendelian consistency. - Tests multiple markers using haplotypes; estimates haplotype frequencies and linkage disequilibrium between pairs of markers. - Offers two multi-marker tests for testing multiple markers simultaneously, without resolving phase or assuming no recombination. - Uses standard pedigree data files; phenotype file is optional. - Offers the Sibs Disequilibrium Test.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/fbat_1.10.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/fbat_1.10.0.zip"
  },
  "puma": {
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      "R (>= 2.6.0)",
      "Biobase (>= 2.5.5)",
      "affy (>= 1.23.4)",
      "graphics",
      "grDevices",
      "methods",
      "stats",
      "utils"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/puma_1.12.0.tgz",
    "Version": "1.12.0",
    "dependsOnMe": [
      "pumadata"
    ],
    "URL": "http://umber.sbs.man.ac.uk/resources/puma",
    "Maintainer": "Richard Pearson <richard.pearson@well.ox.ac.uk>",
    "Author": "Richard D. Pearson, Xuejun Liu, Magnus Rattray, Marta Milo, Neil D. Lawrence, Guido Sanguinetti",
    "Title": "Propagating Uncertainty in Microarray Analysis",
    "source.ver": "src/contrib/puma_1.12.0.tar.gz",
    "Imports": [
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      "affy (>= 1.23.4)"
    ],
    "Suggests": [
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      "affydata",
      "snow",
      "limma",
      "annotate",
      "ROCR"
    ],
    "Package": "puma",
    "vignettes": [
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      "vignettes/puma/inst/doc/puma-015.pdf",
      "vignettes/puma/inst/doc/puma-016.pdf",
      "vignettes/puma/inst/doc/puma-022.pdf",
      "vignettes/puma/inst/doc/puma-023.pdf",
      "vignettes/puma/inst/doc/puma-024.pdf",
      "vignettes/puma/inst/doc/puma.pdf",
      "vignettes/puma/inst/doc/Rplots.pdf"
    ],
    "License": "LGPL",
    "biocViews": [
      "Bioinformatics",
      "Clustering",
      "DifferentialExpression",
      "Microarray",
      "OneChannel",
      "Preprocessing",
      "Software"
    ],
    "Description": "Most analyses of Affymetrix GeneChip data are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting and data manipulation functions.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/puma_1.12.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/puma_1.12.0.zip"
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  "MEDME": {
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      "graphics",
      "methods",
      "stats",
      "utils"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/MEDME_1.6.0.tgz",
    "Version": "1.6.0",
    "Maintainer": "Mattia Pelizzola <mattia.pelizzola@gmail.com>",
    "Author": "Mattia Pelizzola and Annette Molinaro",
    "Title": "Modelling Experimental Data from MeDIP Enrichment",
    "source.ver": "src/contrib/MEDME_1.6.0.tar.gz",
    "Imports": [
      "Biostrings",
      "MASS",
      "drc"
    ],
    "Suggests": [
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      "BSgenome.Mmusculus.UCSC.mm9"
    ],
    "Package": "MEDME",
    "vignettes": [
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    ],
    "License": "GPL (>= 2)",
    "biocViews": [
      "CpGIsland",
      "Microarray",
      "Software"
    ],
    "Description": "MEDME allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/MEDME_1.6.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/MEDME_1.6.0.zip"
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      "Biobase (>= 1.5.0)",
      "methods"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/GeneSpring_2.20.0.tgz",
    "Version": "2.20.0",
    "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_2.20.0.tar.gz",
    "Package": "GeneSpring",
    "vignettes": [
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    ],
    "License": "GPL",
    "biocViews": [
      "Infrastructure",
      "Software"
    ],
    "Description": "Set of functions and class definitions to be able to read and write GeneSpring specific data objects and covert them to BioConductor objects",
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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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    "win.binary.ver": "bin/windows/contrib/2.10/xmapbridge_1.4.0.zip"
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      "R (>= 1.9.0)",
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      "methods"
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    "Version": "1.24.0",
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      "convert",
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      "dyebiasexamples",
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      "nnNorm",
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      "RMAGEML",
      "stepNorm"
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    "URL": "http://www.maths.usyd.edu.au/u/jeany/",
    "Maintainer": "Yee Hwa (Jean) Yang <jean@biostat.ucsf.edu>",
    "Author": "Yee Hwa (Jean) Yang <jeany@maths.usyd.edu.au> with contributions from Agnes Paquet and Sandrine Dudoit.",
    "Title": "Exploratory analysis for two-color spotted microarray data",
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      "hexbin",
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      "Mfuzz"
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      "vignettes/marray/inst/doc/marrayClassesShort.pdf",
      "vignettes/marray/inst/doc/marrayInput.pdf",
      "vignettes/marray/inst/doc/marrayNorm.pdf",
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    "Description": "Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking.",
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      "PLPE"
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    "URL": "http://www.r-project.org,",
    "Maintainer": "Nitin Jain <emailnitinjain@gmail.com>",
    "Author": "Nitin Jain <emailnitinjain@gmail.com>, Michael O'Connell <michaelo@warath.com>, Jae K. Lee <jaeklee@virginia.edu>. Includes R source code contributed by HyungJun Cho <hcho@virginia.edu>",
    "Title": "Methods for analyzing microarray data using Local Pooled Error (LPE) method",
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      "utils"
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    "Package": "LPE",
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    "License": "LGPL",
    "biocViews": [
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    "Description": "This LPE library is used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional 'BH' or 'BY' procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization.  LPE library is primarily used for analyzing data between two conditions. To use it for paired data, see LPEP library. For using LPE in multiple conditions, use HEM library.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/LPE_1.20.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/LPE_1.20.0.zip"
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    "Maintainer": "Biocore Team c/o BioC user list <bioconductor@stat.math.ethz.ch>",
    "Author": "R. Gentleman, Jeff Gentry",
    "Title": "Dynamic document tools",
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    "Imports": [
      "methods"
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    "Package": "DynDoc",
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    "Description": "A set of functions to create and interact with dynamic documents and vignettes.",
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    "win.binary.ver": "bin/windows/contrib/2.10/DynDoc_1.24.0.zip"
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      "graphics",
      "RCurl"
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    "Version": "1.4.0",
    "URL": "http://bioinformatics.oxfordjournals.org/cgi/reprint/btn577v1",
    "Maintainer": "Adi Laurentiu Tarca <atarca@med.wayne.edu>",
    "Author": "Adi Laurentiu Tarca <tarca@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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    "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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    "win.binary.ver": "bin/windows/contrib/2.10/SPIA_1.4.0.zip"
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      "RankProd",
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    "Title": "Statistical analysis of high-throughput RNAi screens",
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      "limma",
      "biomaRt"
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    "biocViews": [
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    "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.",
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    "win.binary.ver": "bin/windows/contrib/2.10/RNAither_1.6.1.zip"
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    "Version": "1.6.0",
    "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",
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    "Package": "PLPE",
    "vignettes": [
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    "License": "GPL (>= 2)",
    "biocViews": [
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      "Microarray",
      "Proteomics",
      "Software"
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    "Description": "This package performs tests for paired high-throughput data.",
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    "win.binary.ver": "bin/windows/contrib/2.10/PLPE_1.6.0.zip"
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      "RBGL"
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    "Maintainer": "Denise Scholtens <dscholtens@northwestern.edu>",
    "Author": "Denise Scholtens <dscholtens@northwestern.edu>",
    "Title": "Estimate protein complex membership using AP-MS protein data",
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    "Imports": [
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    "Package": "apComplex",
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    "License": "LGPL",
    "biocViews": [
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      "MassSpectrometry",
      "Software",
      "Visualization"
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    "Description": "Functions to estimate a bipartite graph of protein complex membership using AP-MS data.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/apComplex_2.12.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/apComplex_2.12.0.zip"
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    "Depends": [
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      "annotate"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/macat_1.20.0.tgz",
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    "Maintainer": "Joern Toedling <joern.toedling@curie.fr>",
    "Author": "Benjamin Georgi, Matthias Heinig, Stefan Roepcke, Sebastian Schmeier, Joern Toedling",
    "Title": "MicroArray Chromosome Analysis Tool",
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      "stjudem"
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      "vignettes/macat/inst/doc/chrom6TkNN.pdf",
      "vignettes/macat/inst/doc/evalkNN6.pdf",
      "vignettes/macat/inst/doc/macat.pdf",
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    "License": "Artistic-2.0",
    "biocViews": [
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      "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'.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/macat_1.20.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/macat_1.20.0.zip"
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      "methods",
      "graphics",
      "stats",
      "utils",
      "abind"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/EBImage_3.2.0.tgz",
    "Version": "3.2.0",
    "Maintainer": "Gregoire Pau <gpau@ebi.ac.uk>",
    "Author": "Oleg Sklyar, Gregoire Pau, Mike Smith, Wolfgang Huber",
    "Title": "Image processing toolbox for R",
    "suggestsMe": [
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    "source.ver": "src/contrib/EBImage_3.2.0.tar.gz",
    "Package": "EBImage",
    "vignettes": [
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    "License": "Artistic-2.0",
    "biocViews": [
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      "Visualization"
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    "Description": "EBImage is an R package which provides general purpose functionality for the reading, writing, processing and analysis of images. Furthermore, in the context of microscopy based cellular assays, EBImage offers tools to transform the images, segment cells and extract quantitative cellular descriptors.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/EBImage_3.2.0.tgz",
    "SystemRequirements": "ImageMagick (>= 6.3.7), GTK+ (> 2.6)",
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      "affy",
      "genefilter",
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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",
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      "ArrayTools"
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    "source.ver": "src/contrib/simpleaffy_2.22.0.tar.gz",
    "Imports": [
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      "genefilter",
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      "stats",
      "utils"
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    "Package": "simpleaffy",
    "vignettes": [
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    "License": "GPL (>= 2)",
    "biocViews": [
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      "DataImport",
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      "Preprocessing",
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      "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...",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/simpleaffy_2.22.0.tgz",
    "importsMe": [
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      "arrayQualityMetrics",
      "yaqcaffy"
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    "win.binary.ver": "bin/windows/contrib/2.10/simpleaffy_2.22.0.zip"
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      "biomaRt",
      "grid"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/GenomeGraphs_1.6.0.tgz",
    "Version": "1.6.0",
    "Maintainer": "Steffen Durinck <steffen@stat.berkeley.edu>",
    "Author": "Steffen Durinck <steffen@stat.berkeley.edu>, James Bullard <bullard@berkeley.edu>",
    "Title": "Plotting genomic information from Ensembl",
    "suggestsMe": [
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    "Package": "GenomeGraphs",
    "vignettes": [
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    "License": "Artistic-2.0",
    "biocViews": [
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    ],
    "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.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/GenomeGraphs_1.6.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/GenomeGraphs_1.6.0.zip"
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      "R (>= 1.9.0)",
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/clusterStab_1.18.0.tgz",
    "Version": "1.18.0",
    "Maintainer": "James W. MacDonald <jmacdon@med.umich.edu>",
    "Author": "James W. MacDonald, Debashis Ghosh, Mark Smolkin",
    "Title": "Compute cluster stability scores for microarray data",
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    "Suggests": [
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    "vignettes": [
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    "License": "Artistic-2.0",
    "biocViews": [
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      "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.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/clusterStab_1.18.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/clusterStab_1.18.0.zip"
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      "survival"
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    "Maintainer": "Rob Tibshirani <tibs@stat.stanford.edu>",
    "Author": "T. Hastie, R. Tibshirani, Balasubramanian Narasimhan, Gil Chu",
    "Title": "Pam: prediction analysis for microarrays",
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      "oneChannelGUI"
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    "source.ver": "src/contrib/pamr_1.44.0.tar.gz",
    "Package": "pamr",
    "License": "GPL-2",
    "biocViews": [
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      "Microarray",
      "Software"
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    "Description": "Some functions for sample classification in microarrays",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/pamr_1.44.0.tgz",
    "importsMe": [
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    "win.binary.ver": "bin/windows/contrib/2.10/pamr_1.44.0.zip"
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      "stats",
      "graphics",
      "grDevices",
      "Biobase",
      "methods"
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    "Maintainer": "Reid F. Thompson <rthompso@aecom.yu.edu>",
    "Author": "Reid F. Thompson <rthompso@aecom.yu.edu>, John M. Greally <jgreally@aecom.yu.edu>, with contributions from Mark Reimers <mreimers@vcu.edu>",
    "Title": "Tools for HELP data analysis",
    "source.ver": "src/contrib/HELP_1.4.0.tar.gz",
    "Package": "HELP",
    "vignettes": [
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    "License": "GPL (>= 2)",
    "biocViews": [
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      "DNAMethylation",
      "DataImport",
      "Microarray",
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      "Software",
      "TwoChannel",
      "Visualization"
    ],
    "Description": "The package contains a modular pipeline for analysis of HELP microarray data, and includes graphical and mathematical tools with more general applications",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/HELP_1.4.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/HELP_1.4.0.zip"
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    "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",
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    "Imports": [
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      "siggenes",
      "genefilter",
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      "GeneMeta"
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    "Package": "XDE",
    "vignettes": [
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      "vignettes/XDE/inst/doc/XdeParameterClass.pdf"
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    "License": "LGPL-2",
    "biocViews": [
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      "DifferentialExpression",
      "Microarray",
      "Software"
    ],
    "Description": "Multi-level model for cross-study detection of differential gene expression.",
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    "win.binary.ver": "bin/windows/contrib/2.10/XDE_1.6.0.zip"
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      "digest",
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      "drosgenome1.db",
      "drosgenome1probe",
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      "drosophila2probe",
      "ecoli2probe",
      "ecoliasv2probe",
      "ecoliK12.db0",
      "ecoliprobe",
      "ecoliSakai.db0",
      "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",
      "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",
      "homolog.db",
      "hs25kresogen.db",
      "Hs6UG171.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",
      "hugene10stprobeset.db",
      "hugene10sttranscriptcluster.db",
      "human.db0",
      "HuO22.db",
      "hwgcod.db",
      "illuminaHumanDASLBeadID.db",
      "IlluminaHumanMethylation27k.db",
      "illuminaHumanv1.db",
      "illuminaHumanv1BeadID.db",
      "illuminaHumanv2.db",
      "illuminaHumanv2BeadID.db",
      "illuminaHumanv3.db",
      "illuminaHumanv3BeadID.db",
      "illuminaMousev1.db",
      "illuminaMousev1BeadID.db",
      "illuminaMousev1p1.db",
      "illuminaMousev1p1BeadID.db",
      "illuminaMousev2.db",
      "illuminaMousev2BeadID.db",
      "illuminaRatv1.db",
      "illuminaRatv1BeadID.db",
      "indac.db",
      "int.did.db",
      "int.domine.db",
      "int.geneint.db",
      "int.intact.db",
      "int.mppi.db",
      "JazaeriMetaData.db",
      "KEGG.db",
      "LAPOINTE.db",
      "lumiHumanAll.db",
      "lumiHumanIDMapping",
      "lumiMouseAll.db",
      "lumiMouseIDMapping",
      "lumiRatAll.db",
      "lumiRatIDMapping",
      "m10kcod.db",
      "m20kcod.db",
      "maizeprobe",
      "malaria.db0",
      "matchprobes",
      "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",
      "mirna10probe",
      "mm24kresogen.db",
      "moe430a.db",
      "moe430aprobe",
      "moe430b.db",
      "moe430bprobe",
      "mogene10stprobeset.db",
      "mogene10sttranscriptcluster.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",
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      "org.Hs.eg.db",
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      "org.Hs.ipi.db",
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      "org.Mm.ipi.db",
      "org.Mm.ref.db",
      "org.Mm.sp.db",
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      "org.Rn.ref.db",
      "org.Rn.sp.db",
      "org.Sc.sgd.db",
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      "org.Xl.eg.db",
      "paeg1aprobe",
      "PAnnBuilder",
      "PartheenMetaData.db",
      "pathRender",
      "pedbarrayv10.db",
      "pedbarrayv9.db",
      "PFAM.db",
      "PGSEA",
      "pig.db0",
      "plasmodiumanophelesprobe",
      "POCRCannotation.db",
      "poplarprobe",
      "porcineprobe",
      "qpgraph",
      "r10kcod.db",
      "rae230a.db",
      "rae230aprobe",
      "rae230b.db",
      "rae230bprobe",
      "ragene10stprobeset.db",
      "ragene10sttranscriptcluster.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",
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    "Maintainer": "Biocore Team c/o BioC user list <bioconductor@stat.math.ethz.ch>",
    "Author": "Herve Pages, Marc Carlson, Seth Falcon, Nianhua Li",
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      "mgu74b.db",
      "mgu74bv2.db",
      "mgu74c.db",
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      "mgug4104a.db",
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      "org.Rn.sp.db",
      "org.Sc.sgd.db",
      "org.Ss.eg.db",
      "org.Xl.eg.db",
      "PartheenMetaData.db",
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      "pedbarrayv9.db",
      "PFAM.db",
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      "POCRCannotation.db",
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      "r10kcod.db",
      "rae230a.db",
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      "ragene10stprobeset.db",
      "ragene10sttranscriptcluster.db",
      "rat.db0",
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      "rgu34a.db",
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      "rguatlas4k.db",
      "rgug4105a.db",
      "rgug4130a.db",
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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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    "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.",
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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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    "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.",
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    "URL": "http://www.microarrays.med.uni-goettingen.de",
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    "Author": "Jobst Landgrebe <jlandgr1@gwdg.de> and Frank Bretz <bretz@bioinf.uni-hannover.de>",
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    "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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      "Software"
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    "Maintainer": "Jitao David Zhang <j.zhang@dkfz.de>",
    "Author": "Rudolf Biczok, Markus Ruschhaupt and Jitao David Zhang",
    "Title": "The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)",
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    "Maintainer": "Mark van de Wiel <mark.vdwiel@vumc.nl>",
    "Author": "Sjoerd Vosse & Mark van de Wiel",
    "Title": "Dimension Reduction for Array CGH Data with Minimal Information Loss.",
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      "Microarray",
      "Software",
      "Visualization"
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    "Maintainer": "Martin Morgan <mtmorgan@fhcrc.org>",
    "Author": "Nianhua Li, MT Morgan",
    "Title": "Expose R functions as web services through Java/Axis/Apache",
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    "biocViews": [
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    "Description": "This package provides mechanisms for automatic function prototyping and exposure of R functionality in a web services environment."
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      "limma",
      "affy",
      "Biobase"
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    "Version": "1.4.0",
    "Maintainer": "Jessica Mar <jess@jimmy.harvard.edu>",
    "Author": "Jessica Mar",
    "Title": "Data-driven normalization strategies for high-throughput qPCR data.",
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    "License": "LGPL (>= 2)",
    "biocViews": [
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      "Preprocessing",
      "Software"
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    "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.",
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    "win.binary.ver": "bin/windows/contrib/2.10/qpcrNorm_1.4.0.zip"
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      "Rgraphviz",
      "RColorBrewer",
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    "URL": "http://www.bioconductor.org",
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    "Author": "Li Long <lilong@isb-sib.ch>",
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      "Biobase",
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    "Maintainer": "Pedro Lopez-Romero <plopez@cnic.es>",
    "Author": "Pedro Lopez-Romero <plopez@cnic.es>",
    "Title": "Processing and Differential Expression Analysis of Agilent microRNA chips",
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    "License": "GPL-3",
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      "DifferentialExpression",
      "Microarray",
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    "win.binary.ver": "bin/windows/contrib/2.10/AgiMicroRna_1.0.0.zip"
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    "Version": "1.0.1",
    "Maintainer": "Bart P.P. van Houte <bvhoute@few.vu.nl>",
    "Author": "Thomas W. Binsl, Bart P.P. van Houte, Hannes Hettling",
    "Title": "Normalization of array CGH data with imbalanced aberrations.",
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    "Imports": [
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      "CGHbase",
      "CGHcall",
      "methods",
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    "License": "GPL (>= 3)",
    "biocViews": [
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      "Software"
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    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/CGHnormaliter_1.0.1.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/CGHnormaliter_1.0.1.zip"
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    "URL": "http://www.braju.com/R/",
    "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",
    "biocViews": [
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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.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/aroma.light_1.14.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/aroma.light_1.14.0.zip"
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    "Version": "1.18.0",
    "URL": "http://www.healthsystem.virginia.edu/internet/hes/biostat/bioinformatics/",
    "Maintainer": "HyungJun Cho <hcho@virginia.edu>",
    "Author": "HyungJun Cho <hcho@virginia.edu> and Jae K. Lee <jaeklee@virginia.edu>",
    "Title": "Heterogeneous error model for identification of differentially expressed genes under multiple conditions",
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    "License": "GPL (>= 2)",
    "biocViews": [
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      "DifferentialExpression",
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    "win.binary.ver": "bin/windows/contrib/2.10/HEM_1.18.0.zip"
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    "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",
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    "License": "LGPL",
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    "Description": "The package contains functions to perform the PDNN method described by Li Zhang et al.",
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    "win.binary.ver": "bin/windows/contrib/2.10/affypdnn_1.20.0.zip"
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    "Maintainer": "James Bullard <bullard@stat.berkeley.edu>",
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    "Title": "Analyze genomic data",
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    "Imports": [
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      "utils"
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    "Package": "Genominator",
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      "vignettes/Genominator/inst/doc/withShortRead.pdf"
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    "License": "Artistic-2.0",
    "biocViews": [
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    "Description": "Tools for storing, accessing, and visualizing genomic data.",
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    "win.binary.ver": "bin/windows/contrib/2.10/Genominator_1.0.3.zip"
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    "Version": "1.22.1",
    "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>,",
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    "License": "GPL (>= 2)",
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    "win.binary.ver": "bin/windows/contrib/2.10/affycomp_1.22.1.zip"
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    "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.",
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    "Package": "GeneR",
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    "License": "CeCILL-2.0",
    "biocViews": [
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    "Description": "Package manipulating nucleotidic sequences (Embl, Fasta, GenBank)",
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    "win.binary.ver": "bin/windows/contrib/2.10/GeneR_2.16.0.zip"
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    "Author": "Weiliang Qiu <weiliang.qiu@gmail.com> and Mei-Ling Ting Lee <meilinglee@sph.osu.edu> and George Alex Whitmore <george.whitmore@mcgill.ca>",
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    "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.",
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    "Author": "Joern Toedling, Oleg Sklyar, Tammo Krueger, Matt Ritchie, Wolfgang Huber",
    "Title": "R Investigation of ChIP-chip Oligoarrays",
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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": "Katherine S. Pollard, with Mark J. van der Laan <laan@stat.berkeley.edu> and Greg Wall",
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    "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.",
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    "win.binary.ver": "bin/windows/contrib/2.10/GeneSelector_2.2.0.zip"
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    "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",
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    "Imports": [
      "Biobase",
      "MASS",
      "graphics",
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      "survival"
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      "ALL"
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    "Description": "Gene selection based on a mixture of marginal distributions",
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    "win.binary.ver": "bin/windows/contrib/2.10/GeneSelectMMD_1.2.0.zip"
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    "Version": "1.6.0",
    "URL": "http://www.ibe.med.uni-muenchen.de",
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    "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",
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    "Suggests": [
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    "Enhances": [
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    "win.binary.ver": "bin/windows/contrib/2.10/affyPara_1.6.0.zip"
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    "Maintainer": "Rodrigo Alvarez-Glez <rodrigo.djv@uvigo.es>",
    "Author": "R. Alvarez-Gonzalez, D. Glez-Pena, F. Diaz, F. Fdez-Riverola",
    "Title": "Gene Selection",
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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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    "Maintainer": "Elizabeth Whalen <ewhalen@hsph.harvard.edu>",
    "Author": "Elizabeth Whalen",
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    "win.binary.ver": "bin/windows/contrib/2.10/BioMVCClass_1.14.0.zip"
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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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    "License": "Artistic-2.0",
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    "Description": "test package for a pathway 'ontology'",
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    "win.binary.ver": "bin/windows/contrib/2.10/keggorth_1.8.0.zip"
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    "Maintainer": "Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>",
    "Author": "Rafael A Irizarry, Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>",
    "Title": "Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.",
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    "Imports": [
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      "preprocessCore",
      "utils",
      "stats",
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      "splines",
      "mvtnorm",
      "oligoClasses",
      "ellipse",
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      "SNPchip"
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    "Suggests": [
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    "vignettes": [
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      "vignettes/crlmm/inst/doc/crlmmDownstream.pdf",
      "vignettes/crlmm/inst/doc/crlmmIllumina.pdf",
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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 6.0.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/crlmm_1.4.5.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/crlmm_1.4.5.zip"
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      "methods"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/baySeq_1.0.0.tgz",
    "Version": "1.0.0",
    "Maintainer": "Thomas J. Hardcastle <tjh48@cam.ac.uk>",
    "Author": "Thomas J. Hardcastle",
    "Title": "Empirical Bayesian analysis of patterns of differential expression in count data",
    "source.ver": "src/contrib/baySeq_1.0.0.tar.gz",
    "Suggests": [
      "snow"
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    "Package": "baySeq",
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    "License": "GPL-3",
    "biocViews": [
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      "DifferentialExpression",
      "HighThroughputSequencing",
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      "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.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/baySeq_1.0.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/baySeq_1.0.0.zip"
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      "Biobase",
      "affy",
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    "Author": "Colin A. Smith <webbioc@colinsmith.org>",
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    "Package": "webbioc",
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    "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.)",
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    "SystemRequirements": "Unix, Perl (>= 5.6.0), Netpbm",
    "win.binary.ver": "bin/windows/contrib/2.10/webbioc_1.18.0.zip"
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      "methods",
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    "Author": "Laurent Gautier <laurent@cbs.dtu.dk>",
    "Title": "splicegear",
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    "Imports": [
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      "Biobase",
      "graphics",
      "grDevices",
      "grid",
      "methods",
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      "XML"
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    "vignettes": [
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    "License": "LGPL",
    "biocViews": [
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    "Description": "A set of tools to work with alternative splicing",
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    "win.binary.ver": "bin/windows/contrib/2.10/splicegear_1.18.0.zip"
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      "R (>= 2.1.0)",
      "MASS"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/RLMM_1.8.0.tgz",
    "Version": "1.8.0",
    "URL": "http://www.stat.berkeley.edu/users/nrabbee/RLMM",
    "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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    "Package": "RLMM",
    "vignettes": [
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    "biocViews": [
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      "SNP",
      "Software"
    ],
    "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.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/RLMM_1.8.0.tgz",
    "SystemRequirements": "Internal files Xba.CQV, Xba.regions (or other regions file)",
    "win.binary.ver": "bin/windows/contrib/2.10/RLMM_1.8.0.zip"
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      "fields",
      "hexbin",
      "lattice",
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      "xgobi",
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    "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",
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    "License": "GPL-2",
    "biocViews": [
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    "Maintainer": "Ernest Turro <ernest.turro@ic.ac.uk>",
    "Author": "Ernest Turro, Graeme Ambler, Anne-Mette K Hein",
    "Title": "Bayesian Gene eXpression",
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    "Suggests": [
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    "License": "GPL",
    "biocViews": [
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    "Description": "Bayesian integrated analysis of Affymetrix GeneChips",
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    "Author": "Carsten Kuhl, Ralf Tautenhahn, Steffen Neumann {ckuhl|rtautenh|sneumann}@ipb-halle.de",
    "Title": "Collection of annotation related methods for mass spectrometry data",
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    "License": "GPL (>= 2)",
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    "win.binary.ver": "bin/windows/contrib/2.10/CAMERA_1.2.0.zip"
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    "Author": "Venkatraman E. Seshan, Adam Olshen",
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    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/DNAcopy_1.20.0.tgz",
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    "Version": "1.4.0",
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    "Author": "J. Zhang and B. Feng",
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    "win.binary.ver": "bin/windows/contrib/2.10/cghMCR_1.4.0.zip"
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    "Title": "Multi sample aCGH analysis package using kernel convolution",
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    "Enhances": [
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    "Description": "Functions and datasets and examples to accompany the monograph R For Bioinformatics.",
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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 thereby genes, of interest.",
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    "URL": "http://www.bioconductor.org",
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    "Description": "Functions for creating PostgreSQL database tables, with auto incrementing primary keys, selection of foreign keys to allow referencial integrity and a logging mechanism.",
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    "Author": "VJ Carey <stvjc@channing.harvard.edu>, BJ Harshfield <rebjh@channing.harvard.edu>, S Falcon <sfalcon@fhcrc.org>",
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    "Author": "Gregory Warnes <warnes@bst.rochester.edu> Ross Lazarus <ross.lazarus@channing.harvard.edu> Scott D Chasalow <scott.chasalow@bms.com> Giovanni Montana <giovanni.montana@bms.com> Michael O'Connell <moconnell@insightful.com> Junsheng Cheng <jcheng8@users.sourceforge.net> Nitin Jain <nitin.jain@pfizer.com>",
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      "vignettes/GeneticsBase/inst/doc/CAMP_LD_html.pdf",
      "vignettes/GeneticsBase/inst/doc/HOWTO-LoadGenotypes.pdf",
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    "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>.",
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    "URL": "http://www.dkfz.de/mga/whuber, http://www.dkfz.de/LIFEdb",
    "Maintainer": "Florian Hahne <fhahne@fhcrc.org>",
    "Author": "Florian Hahne <fhahne@fhcrc.org>, Wolfgang Huber <huber@ebi.ac.uk>, Markus Ruschhaupt, Joern Toedling <toedling@ebi.ac.uk>",
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    "Author": "Seth Falcon, Benilton Carvalho with contributions by Vince Carey and Matt Settles",
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    "Maintainer": "Holger Froehlich <h.froehlich@dkfz.de>",
    "Author": "Holger Froehlich <h.froehlich@dkfz.de>, contributions by Tim Beissbarth <t.beissbarth@dkfz.de>",
    "Title": "Prediction of KEGG pathway membership for individual genes based on InterPro domain signatures",
    "source.ver": "src/contrib/gene2pathway_1.4.0.tar.gz",
    "Imports": [
      "SSOAP",
      "RCurl"
    ],
    "Package": "gene2pathway",
    "vignettes": [
      "vignettes/gene2pathway/inst/doc/gene2pathway.pdf"
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    "License": "GPL (>= 2)",
    "biocViews": [
      "Bioinformatics",
      "Classification",
      "GraphsAndNetworks",
      "Microarray",
      "Pathways",
      "Software"
    ],
    "Description": "The package takes a list of genes and predicts to which KEGG pathway each gene maps to. This is done by looking at the InterPro domains of each gene. Each prediction is assigned a confidence score. The package also allows to predict connected component membership of genes within signaling pathways. Separate models for each organism supported by KEGG can be trained.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/gene2pathway_1.4.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/gene2pathway_1.4.0.zip"
  },
  "exonmap": {
    "Depends": [
      "R (>= 2.0)",
      "affy (>= 1.23.4)",
      "genefilter",
      "RColorBrewer",
      "RMySQL (>= 0.6-0)",
      "DBI",
      "methods"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/exonmap_2.4.0.tgz",
    "Version": "2.4.0",
    "URL": "http://www.bioconductor.org, http://bioinformatics.picr.man.ac.uk",
    "Maintainer": "Crispin Miller <cmiller@picr.man.ac.uk>",
    "Author": "Crispin J Miller Michal Okoniewski, Tim Yates",
    "Title": "High level analysis of Affymetrix exon array data",
    "source.ver": "src/contrib/exonmap_2.4.0.tar.gz",
    "Package": "exonmap",
    "vignettes": [
      "vignettes/exonmap/inst/doc/exonmap.example.pdf",
      "vignettes/exonmap/inst/doc/exonmap.pdf",
      "vignettes/exonmap/inst/doc/INSTALL.pdf"
    ],
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      "DataImport",
      "DifferentialExpression",
      "Microarray",
      "OneChannel",
      "Preprocessing",
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      "Software",
      "Transcription",
      "Visualization"
    ],
    "Description": "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.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/exonmap_2.4.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/exonmap_2.4.0.zip"
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      "R (>= 2.5)",
      "affy",
      "ecoliLeucine",
      "ecolicdf",
      "Biobase"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/ecolitk_1.18.0.tgz",
    "Version": "1.18.0",
    "Maintainer": "Laurent <lgautier@gmail.com>",
    "Author": "Laurent Gautier",
    "Title": "Meta-data and tools for E. coli",
    "source.ver": "src/contrib/ecolitk_1.18.0.tar.gz",
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      "graph",
      "matchprobes",
      "multtest",
      "vsn"
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    "License": "GPL (>= 2)",
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    "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.",
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    "win.binary.ver": "bin/windows/contrib/2.10/ecolitk_1.18.0.zip"
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    "Depends": [
      "methods",
      "corpcor",
      "globaltest"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/GlobalAncova_3.12.0.tgz",
    "Version": "3.12.0",
    "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",
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    "Imports": [
      "annotate",
      "AnnotationDbi"
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      "GO.db",
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      "hu6800.db",
      "vsn"
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      "vignettes/GlobalAncova/inst/doc/GlobalAncovaDecomp.pdf"
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    "License": "GPL (>= 2)",
    "biocViews": [
      "Bioinformatics",
      "DifferentialExpression",
      "Microarray",
      "OneChannel",
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      "Software"
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    "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.",
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    "win.binary.ver": "bin/windows/contrib/2.10/GlobalAncova_3.12.0.zip"
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      "R (>= 2.6.0)",
      "affyio",
      "oligo"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/makePlatformDesign_1.10.0.tgz",
    "Version": "1.10.0",
    "Maintainer": "Benilton Carvalho <bcarvalh@jhsph.edu>",
    "Author": "Benilton Carvalho <bcarvalh@jhsph.edu>, Rafael A. Irizarry <rafa@jhu.edu> and Ben Bolstad with contributions from Vince Carey, Robert Gentleman, Wolfgang Huber",
    "Title": "Platform Design Package",
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      "maqcExpression4plex"
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      "TwoChannel"
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    "Description": "makePlatformDesign creates the Platform Design environments (PDenvs) required by oligo.",
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    "win.binary.ver": "bin/windows/contrib/2.10/makePlatformDesign_1.10.0.zip"
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      "simpleaffy"
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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",
    "Title": "genefilter: methods for filtering genes from microarray experiments",
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    "Description": "Some basic functions for filtering genes",
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    "win.binary.ver": "bin/windows/contrib/2.10/genefilter_1.28.2.zip"
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      "affy (>= 1.23.4)",
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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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    "Suggests": [
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      "estrogen",
      "annaffy",
      "gcrma"
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    "Package": "AffyExpress",
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    "License": "LGPL",
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      "Visualization"
    ],
    "Description": "The purpose of this package is to provide a comprehensive and easy-to-use tool for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/AffyExpress_1.12.0.tgz",
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    "Author": "Jianhua Zhang",
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    "Suggests": [
      "Biobase"
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    "Package": "widgetTools",
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    "biocViews": [
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      "Software"
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    "Description": "This packages contains tools to support the construction of tcltk widgets",
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    "win.binary.ver": "bin/windows/contrib/2.10/widgetTools_1.24.0.zip"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/SMAP_1.10.1.tgz",
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    "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_1.10.1.tar.gz",
    "Package": "SMAP",
    "vignettes": [
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    ],
    "License": "GPL-2",
    "biocViews": [
      "CopyNumberVariants",
      "Microarray",
      "Software",
      "TwoChannel"
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    "Description": "Functions and classes for DNA copy number profiling of array-CGH data",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/SMAP_1.10.1.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/SMAP_1.10.1.zip"
  },
  "Rolexa": {
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      "R (>= 2.9.0)",
      "mclust",
      "graphics",
      "grDevices",
      "methods",
      "ShortRead"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/Rolexa_1.2.0.tgz",
    "Version": "1.2.0",
    "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_1.2.0.tar.gz",
    "Imports": [
      "Biostrings",
      "graphics",
      "grDevices",
      "IRanges",
      "methods",
      "ShortRead",
      "stats"
    ],
    "Package": "Rolexa",
    "vignettes": [
      "vignettes/Rolexa/inst/doc/Rolexa-vignette.pdf"
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    "License": "GPL-2",
    "biocViews": [
      "DataImport",
      "Preprocessing",
      "QualityControl",
      "Sequencing",
      "Software"
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    "Description": "Provides probabilistic base calling, quality checks and diagnostic plots for Solexa sequencing data",
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    "Enhances": [
      "fork"
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    "win.binary.ver": "bin/windows/contrib/2.10/Rolexa_1.2.0.zip"
  },
  "impute": {
    "Depends": [
      "R (>= 1.7.0)"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/impute_1.20.0.tgz",
    "Version": "1.20.0",
    "Maintainer": "Balasubramanian Narasimhan <naras@stat.Stanford.EDU>",
    "Author": "Trevor Hastie, Robert Tibshirani, Balasubramanian Narasimhan, Gilbert Chu",
    "Title": "impute: Imputation for microarray data",
    "source.ver": "src/contrib/impute_1.20.0.tar.gz",
    "Package": "impute",
    "License": "GPL-2",
    "biocViews": [
      "Bioinformatics",
      "Microarray",
      "Software"
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    "Description": "Imputation for microarray data (currently KNN only)",
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    "win.binary.ver": "bin/windows/contrib/2.10/impute_1.20.0.zip"
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      "Biobase"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/GSEAlm_1.6.0.tgz",
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    "Maintainer": "Assaf Oron <assaf.oron@gmail.com>",
    "Author": "Assaf Oron, Robert Gentleman (with contributions from S. Falcon and Z. Jiang)",
    "Title": "Linear Model Toolset for Gene Set Enrichment Analysis",
    "source.ver": "src/contrib/GSEAlm_1.6.0.tar.gz",
    "Suggests": [
      "GSEABase",
      "Category",
      "multtest",
      "ALL",
      "annotate",
      "hgu95av2.db",
      "genefilter",
      "GOstats",
      "RColorBrewer"
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    "Package": "GSEAlm",
    "vignettes": [
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    "License": "Artistic-2.0",
    "biocViews": [
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      "Microarray",
      "Software"
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    "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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    "win.binary.ver": "bin/windows/contrib/2.10/GSEAlm_1.6.0.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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    "Package": "vsn",
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    "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.",
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    "Maintainer": "J. Zhang <jzhang@jimmy.harvard.edu>",
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    "Title": "R based tk widgets",
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      "affy (>= 1.23.4)",
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    "Version": "1.16.0",
    "Maintainer": "Peter Warren <peter.warren@verizon.net>",
    "Author": "Peter Warren",
    "Title": "Presence-Absence Calls from Negative Strand Matching Probesets",
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    "Package": "panp",
    "vignettes": [
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    "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.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/panp_1.16.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/panp_1.16.0.zip"
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      "Biobase",
      "quantreg"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/OutlierD_1.10.0.tgz",
    "Version": "1.10.0",
    "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_1.10.0.tar.gz",
    "Package": "OutlierD",
    "vignettes": [
      "vignettes/OutlierD/inst/doc/OutlierD.pdf"
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    "License": "GPL (>= 2)",
    "biocViews": [
      "Bioinformatics",
      "Microarray",
      "Software"
    ],
    "Description": "This package detects outliers using quantile regression on the M-A scatterplots of high-throughput data.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/OutlierD_1.10.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/OutlierD_1.10.0.zip"
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  "KEGGSOAP": {
    "Depends": [
      "methods"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/KEGGSOAP_1.20.0.tgz",
    "Version": "1.20.0",
    "dependsOnMe": [
      "gene2pathway"
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    "Maintainer": "Robert Gentleman <rgentlem@fhcrc.org>",
    "Author": "J. Zhang and R. Gentleman",
    "Title": "Client-side SOAP access KEGG",
    "source.ver": "src/contrib/KEGGSOAP_1.20.0.tar.gz",
    "Imports": [
      "XML",
      "RCurl",
      "SSOAP (>= 0.2-2)"
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    "Package": "KEGGSOAP",
    "License": "BSD",
    "biocViews": [
      "Annotation",
      "Pathways",
      "Software"
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    "Description": "A package that provides a client interface to the KEGG SOAP server",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/KEGGSOAP_1.20.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/KEGGSOAP_1.20.0.zip"
  },
  "BufferedMatrixMethods": {
    "Depends": [
      "R (>= 2.6.0)",
      "BufferedMatrix (>= 1.3.0)",
      "methods"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/BufferedMatrixMethods_1.10.1.tgz",
    "Version": "1.10.1",
    "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",
    "source.ver": "src/contrib/BufferedMatrixMethods_1.10.1.tar.gz",
    "Suggests": [
      "affyio",
      "affy"
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    "Package": "BufferedMatrixMethods",
    "License": "GPL (>= 2)",
    "LinkingTo": "BufferedMatrix",
    "biocViews": [
      "Infrastructure",
      "Software"
    ],
    "Description": "Microarray analysis methods that use BufferedMatrix objects",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/BufferedMatrixMethods_1.10.1.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/BufferedMatrixMethods_1.10.1.zip"
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  "GEOmetadb": {
    "Depends": [
      "GEOquery",
      "RSQLite"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/GEOmetadb_1.6.0.tgz",
    "Version": "1.6.0",
    "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_1.6.0.tar.gz",
    "Package": "GEOmetadb",
    "vignettes": [
      "vignettes/GEOmetadb/inst/doc/GEOmetadb_diagram.pdf",
      "vignettes/GEOmetadb/inst/doc/GEOmetadb.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "Infrastructure",
      "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 .",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/GEOmetadb_1.6.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/GEOmetadb_1.6.0.zip"
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  "flowFlowJo": {
    "Depends": [
      "R (>= 2.5.0)",
      "flowCore"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/flowFlowJo_1.4.0.tgz",
    "Version": "1.4.0",
    "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_1.4.0.tar.gz",
    "Imports": [
      "Biobase",
      "flowCore",
      "XML (>= 1.96)",
      "methods",
      "stats",
      "utils"
    ],
    "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.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/flowFlowJo_1.4.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/flowFlowJo_1.4.0.zip"
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  "spikeLI": {
    "Depends": [
      "utils"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/spikeLI_2.6.0.tgz",
    "Version": "2.6.0",
    "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_2.6.0.tar.gz",
    "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).",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/spikeLI_2.6.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/spikeLI_2.6.0.zip"
  },
  "multtest": {
    "Depends": [
      "R (>= 2.9.0)",
      "methods",
      "Biobase"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/multtest_2.2.0.tgz",
    "Version": "2.2.0",
    "dependsOnMe": [
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      "aCGH",
      "adSplit",
      "BicARE",
      "ChIPpeakAnno",
      "KCsmart",
      "LMGene",
      "OCplus",
      "SAGx",
      "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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      "BiocCaseStudies",
      "ecolitk",
      "GeneSelector",
      "GlobalAncova",
      "GOstats",
      "GSEAlm",
      "maigesPack",
      "oneChannelGUI",
      "pcot2",
      "safe",
      "SSPA",
      "topGO",
      "xcms"
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    "Imports": [
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      "MASS"
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    "Package": "multtest",
    "vignettes": [
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      "vignettes/multtest/inst/doc/MTPALL.pdf",
      "vignettes/multtest/inst/doc/multtest.pdf"
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    "License": "LGPL",
    "biocViews": [
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      "Microarray",
      "MultipleComparisons",
      "Software"
    ],
    "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.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/multtest_2.2.0.tgz",
    "Enhances": [
      "snow",
      "Rmpi",
      "rpvm"
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    "importsMe": [
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      "ChIPpeakAnno",
      "globaltest"
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    "win.binary.ver": "bin/windows/contrib/2.10/multtest_2.2.0.zip"
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    "Depends": [
      "R (>= 2.2.0)",
      "survival",
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      "MASS",
      "methods"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/MergeMaid_2.18.0.tgz",
    "Version": "2.18.0",
    "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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      "XDE"
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    "source.ver": "src/contrib/MergeMaid_2.18.0.tar.gz",
    "Package": "MergeMaid",
    "vignettes": [
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    "License": "GPL (>= 2)",
    "biocViews": [
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      "Visualization"
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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.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/MergeMaid_2.18.0.tgz",
    "importsMe": [
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    "win.binary.ver": "bin/windows/contrib/2.10/MergeMaid_2.18.0.zip"
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  "chipseq": {
    "Depends": [
      "methods",
      "IRanges (>= 1.3.77)",
      "BSgenome",
      "ShortRead",
      "lattice"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/chipseq_0.2.1.tgz",
    "Version": "0.2.1",
    "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",
    "source.ver": "src/contrib/chipseq_0.2.1.tar.gz",
    "Imports": [
      "BSgenome",
      "IRanges",
      "lattice",
      "methods",
      "ShortRead",
      "stats"
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    "Suggests": [
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      "GenomicFeatures.Mmusculus.UCSC.mm9",
      "GenomicFeatures.Hsapiens.UCSC.hg18",
      "BSgenome.Mmusculus.UCSC.mm9"
    ],
    "Package": "chipseq",
    "vignettes": [
      "vignettes/chipseq/inst/doc/Workflow.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "Bioinformatics",
      "Infrastructure",
      "Software"
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    "Description": "Tools for helping process short read data for chipseq experiments",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/chipseq_0.2.1.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/chipseq_0.2.1.zip"
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  "CGHbase": {
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      "R (>= 2.4.0)",
      "methods",
      "Biobase (>= 2.5.5)",
      "marray"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/CGHbase_1.4.0.tgz",
    "Version": "1.4.0",
    "dependsOnMe": [
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      "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_1.4.0.tar.gz",
    "Package": "CGHbase",
    "License": "GPL",
    "biocViews": [
      "CopyNumberVariants",
      "Infrastructure",
      "Microarray",
      "Software"
    ],
    "Description": "Contains functions and classes that are needed by arrayCGH packages.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/CGHbase_1.4.0.tgz",
    "importsMe": [
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    "win.binary.ver": "bin/windows/contrib/2.10/CGHbase_1.4.0.zip"
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    "Depends": [
      "graph",
      "methods"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/RBGL_1.22.0.tgz",
    "Version": "1.22.0",
    "dependsOnMe": [
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      "gene2pathway",
      "pkgDepTools",
      "RpsiXML"
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    "URL": "http://www.bioconductor.org",
    "Maintainer": "Li Long <li.long@isb-sib.ch>",
    "Author": "Vince Carey <stvjc@channing.harvard.edu>, Li Long <li.long@isb-sib.ch>, R. Gentleman",
    "Title": "An interface to the BOOST graph library",
    "suggestsMe": [
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      "graph",
      "KEGGgraph",
      "keggorth",
      "yeastExpData"
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    "Imports": [
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    "Package": "RBGL",
    "vignettes": [
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      "vignettes/RBGL/inst/doc/RBGL.pdf"
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    "License": "Artistic-2.0",
    "biocViews": [
      "GraphsAndNetworks",
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    ],
    "Description": "A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/RBGL_1.22.0.tgz",
    "importsMe": [
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      "Category",
      "GOstats",
      "nem",
      "pkgDepTools"
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    "win.binary.ver": "bin/windows/contrib/2.10/RBGL_1.22.0.zip"
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    "Depends": [
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      "methods",
      "Biobase (>= 2.5.5)"
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    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/PGSEA_1.14.0.tgz",
    "Version": "1.14.0",
    "Maintainer": "Karl Dykema <karl.dykema@vai.org>",
    "Author": "Kyle Furge <kyle.furge@vai.org> and Karl Dykema <karl.dykema@vai.org>",
    "Title": "Parametric Gene Set Enrichment Analysis",
    "source.ver": "src/contrib/PGSEA_1.14.0.tar.gz",
    "Suggests": [
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      "GSEABase",
      "KEGG.db",
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      "Ruuid"
    ],
    "Package": "PGSEA",
    "vignettes": [
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      "vignettes/PGSEA/inst/doc/PGSEA2.pdf"
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    "License": "GPL-2",
    "biocViews": [
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      "Software"
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    "Description": "Parametric Analysis of Gene Set Enrichment",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/PGSEA_1.14.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/PGSEA_1.14.0.zip"
  },
  "arrayMvout": {
    "Depends": [
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      "tools",
      "methods",
      "utils",
      "parody",
      "Biobase",
      "affy",
      "lumi"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/arrayMvout_1.4.0.tgz",
    "Version": "1.4.0",
    "Maintainer": "V. Carey <stvjc@channing.harvard.edu>",
    "Author": "Z. Gao, A. Asare, R. Wang, V. Carey",
    "Title": "multivariate outlier detection for expression array QA",
    "source.ver": "src/contrib/arrayMvout_1.4.0.tar.gz",
    "Imports": [
      "simpleaffy",
      "mdqc",
      "affyContam"
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    "Suggests": [
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      "mvoutData",
      "lumiBarnes",
      "affyPLM",
      "affydata",
      "hgu133atagcdf"
    ],
    "Package": "arrayMvout",
    "vignettes": [
      "vignettes/arrayMvout/inst/doc/arrayMvout-asdad.pdf",
      "vignettes/arrayMvout/inst/doc/arrayMvout-lkadas.pdf",
      "vignettes/arrayMvout/inst/doc/arrayMvout-lkda.pdf",
      "vignettes/arrayMvout/inst/doc/arrayMvout.pdf"
    ],
    "License": "Artistic-2.0",
    "biocViews": [
      "Bioinformatics",
      "Infrastructure",
      "Microarray",
      "QualityControl",
      "Software"
    ],
    "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",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/arrayMvout_1.4.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/arrayMvout_1.4.0.zip"
  },
  "LiquidAssociation": {
    "Depends": [
      "geepack",
      "methods",
      "yeastCC",
      "org.Sc.sgd.db"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/LiquidAssociation_1.0.0.tgz",
    "Version": "1.0.0",
    "Maintainer": "Yen-Yi Ho <yho@jhsph.edu>",
    "Author": "Yen-Yi Ho <yho@jhsph.edu>",
    "Title": "LiquidAssociation",
    "source.ver": "src/contrib/LiquidAssociation_1.0.0.tar.gz",
    "Package": "LiquidAssociation",
    "vignettes": [
      "vignettes/LiquidAssociation/inst/doc/LiquidAssociation.pdf"
    ],
    "License": "GPL (>=3)",
    "biocViews": [
      "Bioinformatics",
      "CellBiology",
      "GeneExpression",
      "Genetics",
      "Pathways",
      "Software",
      "TimeCourse"
    ],
    "Description": "The package contains functions for calculate direct and model-based estimators for liquid associaiton. It also provides functions for testing the existence of liquid associaiton given a gene triplet data.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/LiquidAssociation_1.0.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/LiquidAssociation_1.0.0.zip"
  },
  "RpsiXML": {
    "Depends": [
      "methods",
      "annotate (>= 1.21.0)",
      "graph (>= 1.21.0)",
      "Biobase",
      "RBGL (>= 1.17.0)",
      "XML (>= 2.4.0)",
      "hypergraph (>= 1.15.2)",
      "AnnotationDbi"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/RpsiXML_1.6.0.tgz",
    "Version": "1.6.0",
    "dependsOnMe": [
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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",
    "source.ver": "src/contrib/RpsiXML_1.6.0.tar.gz",
    "Suggests": [
      "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"
    ],
    "Package": "RpsiXML",
    "vignettes": [
      "vignettes/RpsiXML/inst/doc/RpsiXML.pdf",
      "vignettes/RpsiXML/inst/doc/RpsiXMLApp.pdf"
    ],
    "License": "LGPL-3",
    "biocViews": [
      "Infrastructure",
      "Proteomics",
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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.",
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    "Maintainer": "Benjamin Milo Bolstad <bmb@bmbolstad.com>",
    "Author": "Benjamin Milo Bolstad <bmb@bmbolstad.com>",
    "Title": "Tools for parsing Affymetrix data files",
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    "Description": "Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats.",
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    "Maintainer": "Peter Humburg <Peter.Humburg@csiro.au>",
    "Author": "Peter Humburg",
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    "Author": "Yann Ruffieux, contributions from Debjani Bhowmick, Anthony C. Davison, and Darlene R. Goldstein",
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    "Author": "Robert Scharpf <rscharpf@jhsph.edu>, Kevin Scharpf, and Ingo Ruczinski <ingo@jhsph.edu>",
    "Title": "A Hidden Markov Model for high throughput genotyping arrays",
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      "SNP",
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    "Title": "PostgreSQL access",
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    "Description": "Provides methods for accessing data stored in PostgreSQL tables. Code written by Timothy H. Keitt and modified by Jianhua Zhang",
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    "Maintainer": "Li Hong <sysptm@gmail.com>",
    "Author": "Li Hong lihong@sibs.ac.cn",
    "Title": "Protein annotation data package builder",
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    "Description": "Processing annotation data from public data repositories and building annoation data packages.",
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      "org.Rn.ref.db",
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    "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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    "Author": "R. Gentleman and S. Falcon",
    "Title": "Tools for manipulating GO and microarrays.",
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    "Suggests": [
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    "Description": "A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations.",
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    "Maintainer": "Holger Schwender <holger.schw@gmx.de>",
    "Author": "Holger Schwender",
    "Title": "Identification of SNP Interactions",
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    "Suggests": [
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    "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.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/logicFS_1.16.0.tgz",
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      "affy",
      "altcdfenvs"
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    "URL": "http://asterion.rockefeller.edu/Harshlight/",
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    "Author": "Mayte Suarez-Farinas, Maurizio Pellegrino, Knut M. Wittkowski, Marcelo O. Magnasco",
    "Title": "A \"corrective make-up\" program for microarray chips",
    "source.ver": "src/contrib/Harshlight_1.16.0.tar.gz",
    "Package": "Harshlight",
    "vignettes": [
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    "License": "GPL (>= 2)",
    "biocViews": [
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    "Description": "The package is used to detect extended, diffuse and compact blemishes on microarray chips. Harshlight automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection. The new version handle the substitue value as whole matrix to solve the memory problem.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/Harshlight_1.16.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/Harshlight_1.16.0.zip"
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      "annotate",
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      "RSQLite",
      "MASS"
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      "lumiRatIDMapping",
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      "MAQCsubsetILM",
      "mvoutData"
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    "Maintainer": "Pan Du <dupan@northwestern.edu>",
    "Author": "Pan Du, Gang Feng, Warren Kibbe, Simon Lin",
    "Title": "BeadArray Specific Methods for Illumina Microarrays",
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    "Suggests": [
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    "Package": "lumi",
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      "vignettes/lumi/inst/doc/IlluminaAnnotation.pdf",
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      "vignettes/lumi/inst/doc/lumi.pdf"
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    "License": "LGPL (>= 2)",
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    "Description": "The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level.",
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    "Maintainer": "Philippe Hupe <glad@curie.fr>",
    "Author": "Philippe Hupe",
    "Title": "Gain and Loss Analysis of DNA",
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    "Suggests": [
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      "tcltk"
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    "Package": "GLAD",
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    "License": "GPL",
    "biocViews": [
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      "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.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/GLAD_2.6.0.tgz",
    "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'.",
    "win.binary.ver": "bin/windows/contrib/2.10/GLAD_2.6.0.zip"
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    "Title": "Measurement Error model estimate for correlation coefficient",
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    "Package": "MeasurementError.cor",
    "vignettes": [
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    "License": "LGPL",
    "biocViews": [
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      "Software"
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    "Description": "Two-stage measurement error model for correlation estimation with smaller bias than the usual sample correlation",
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    "win.binary.ver": "bin/windows/contrib/2.10/MeasurementError.cor_1.18.0.zip"
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    "Author": "Laurent Gautier <lgautier@gmail.com>",
    "Title": "alternative CDF environments (aka probeset mappings)",
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    "Suggests": [
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    "Package": "altcdfenvs",
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    "License": "GPL (>= 2)",
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    "Description": "Convenience data structures and functions to handle cdfenvs",
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    "Version": "1.20.0",
    "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",
    "source.ver": "src/contrib/DEDS_1.20.0.tar.gz",
    "Package": "DEDS",
    "vignettes": [
      "vignettes/DEDS/inst/doc/DEDS.pdf"
    ],
    "License": "LGPL",
    "biocViews": [
      "Bioinformatics",
      "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.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/DEDS_1.20.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/DEDS_1.20.0.zip"
  },
  "MANOR": {
    "Depends": [
      "R(>= 1.8.0)",
      "GLAD"
    ],
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.10/MANOR_1.18.0.tgz",
    "Version": "1.18.0",
    "URL": "http://bioinfo.curie.fr/projects/manor/index.html",
    "Maintainer": "Pierre Neuvial <pierre.neuvial@curie.fr>",
    "Author": "Pierre Neuvial <pierre.neuvial@curie.fr>, Philippe Hupe <philippe.hupe@curie.fr>",
    "Title": "CGH Micro-Array NORmalization",
    "source.ver": "src/contrib/MANOR_1.18.0.tar.gz",
    "Package": "MANOR",
    "vignettes": [
      "vignettes/MANOR/inst/doc/MANOR.pdf"
    ],
    "License": "GPL",
    "biocViews": [
      "CopyNumberVariants",
      "DataImport",
      "Microarray",
      "Preprocessing",
      "QualityControl",
      "Software",
      "TwoChannel"
    ],
    "Description": "We propose importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH experiments.",
    "mac.binary.universal.ver": "bin/macosx/universal/contrib/2.10/MANOR_1.18.0.tgz",
    "win.binary.ver": "bin/windows/contrib/2.10/MANOR_1.18.0.zip"
  }
}