{
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    "Author": "Stefanie Scheid <stefanie.scheid@gmx.de>",
    "Title": "Estimation of local false discovery rate",
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    "Author": "HyungJun Cho <hj4cho@korea.ac.kr>",
    "Title": "Outlier detection using quantile regression on the M-A scatterplots of high-throughput data",
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    "Author": "Raffale A Calogero, Bioinformatics and Genomics Unit, Molecular Biotechnology Center, Torino (Italy)",
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      "rtracklayer",
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      "goseq",
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      "mogene10sttranscriptcluster.db",
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      "vignettes/oneChannelGUI/inst/doc/install.pdf",
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      "RNAseq",
      "Software",
      "Statistics"
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    "Description": "This package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code. This library provides a graphical interface for microarray gene and exon level analysis as well as miRNA/mRNA-seq data analysis.",
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    "URL": "http://www.kuicr.kyoto-u.ac.jp/~diez",
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    "Author": "Diego Diez <diego10ruiz@gmail.com>",
    "Title": "Manipulation of Codelink Bioarrays data.",
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    "Package": "codelink",
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      "Software"
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    "Description": "This packages allow reading into R of Codelink bioarray data exported as text from the Codelink software. Also includes some functions to ease the manipulation and pre-processing of data, such in background correction and normalization.",
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    "win.binary.ver": "bin/windows/contrib/2.16/codelink_1.27.0.zip"
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    "Author": "Mike Jiang,Greg Finak,N. Gopalakrishnan",
    "Title": "ncdfFlow: A package that provides ncdf based storage for flow cytometry data.",
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    "biocViews": [
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    "Description": "Provides netCDF storage based methods and functions for manipulation of flow cytometry data.",
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    "Author": "James Bullard, Kasper Daniel Hansen",
    "Title": "Analyze, manage and store genomic data",
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      "Biostrings",
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    "Description": "A package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since it will extract probe level data using the Affymetrix Power Tools application and wrap these data into a ProbeLevelSet. A ProbeLevelSet directly extends the expressionSet, but includes additional information about the sequence of each probe and the probe set it is derived from. The package includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data.",
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    "Title": "Isotopic peak pattern deconvolution for Protein Mass Spectrometry by template matching",
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    "Description": "The package provides functionality to extract isotopic peak patterns from raw mass spectra. This is done by fitting a large set of template basis functions to the raw spectrum using either nonnegative least squares or least absolute deviation fittting. The package offers a flexible function which tries to estimate model parameters in a way tailored to the peak shapes in the data. The package also provides functionality to process LCMS runs.",
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    "Description": "High-throughput sequencing technologies allow the production of large volumes of short sequences, which can be aligned to the genome to create a set of matches to the genome. By looking for regions of the genome which to which there are high densities of matches, we can infer a segmentation of the genome into regions of biological significance. The methods in this package allow the simultaneous segmentation of data from multiple samples, taking into account replicate data, in order to create a consensus segmentation. This has obvious applications in a number of classes of sequencing experiments, particularly in the discovery of small RNA loci and novel mRNA transcriptome discovery.",
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    "Description": "This package contains a targeted clustering algorithm for the analysis of microarray data. The algorithm can aid in the discovery of new genes with similar functions to a given list of genes already known to have closely related functions.",
    "hasLICENSE": false,
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    "Author": "Tengfei Yin, Dianne Cook, Michael Lawrence",
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    "Maintainer": "Martin Morgan <mtmorgan@fhcrc.org>",
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    "Imports": [
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    "Maintainer": "Magnus Astrand <magnus.astrand@astrazeneca.com>",
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    "Maintainer": "Sepp Hochreiter <hochreit@bioinf.jku.at>",
    "Author": "Sepp Hochreiter <hochreit@bioinf.jku.at>",
    "Title": "hapFabia: Identification of very short segments of identity by descent (IBD) characterized by rare variants in large sequencing data",
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    "Description": "A package to identify very short IBD segments in large sequencing data by FABIA biclustering. Two haplotypes are identical by descent (IBD) if they share a segment that both inherited from a common ancestor. Current IBD methods reliably detect long IBD segments because many minor alleles in the segment are concordant between the two haplotypes. However, many cohort studies contain unrelated individuals which share only short IBD segments. This package provides software to identify short IBD segments in sequencing data. Knowledge of short IBD segments are relevant for phasing of genotyping data, association studies, and for population genetics, where they shed light on the evolutionary history of humans. The package supports VCF formats, is based on sparse matrix operations, and provides visualization of haplotype clusters in different formats.",
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    "Title": "Easy extraction of individual probes in Affymetrix tiling arrays",
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    "URL": "http://www.tbi.univie.ac.at/~ivo/RNA/",
    "Maintainer": "Zhenpeng Li <zpli21@gmail.com>",
    "Author": "Zhenpeng Li, Fei Li, Xiaochen Bo and Shengqi Wang",
    "Title": "Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm",
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    "Description": "R based Genetic algorithm for gene expression optimization by considering both mRNA secondary structure and codon usage bias, GeneGA includes the information of highly expressed genes of almost 200 genomes. Meanwhile, Vienna RNA Package is needed to ensure GeneGA to function properly.",
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    "Description": "Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg.",
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  "domainsignatures": {
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    "Author": "Cory Barr, Thomas Wu, Michael Lawrence",
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    "Description": "GSNAP and GMAP are a pair of tools to align short-read data written by Tom Wu.  This package provides convenience methods to work with GMAP and GSNAP from within R. In addition, it provides methods to tally alignment results on a per-nucleotide basis using the bam_tally tool.",
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      "DESeq"
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    "biocViews": [
      "Annotation",
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    ],
    "Description": "The gCMAP package provides a toolkit for comparing differential gene expression profiles through gene set enrichment analysis. Starting from normalized microarray or RNA-seq gene expression values (stored in lists of ExpressionSet and CountDataSet objects) the package performs differential expression analysis using the limma or DESeq packages. Supplying a simple list of gene identifiers, global differential expression profiles or data from complete experiments as input, users can use a unified set of several well-known gene set enrichment analysis methods to retrieve experiments with similar changes in gene expression. To take into account the directionality of gene expression changes, gCMAPQuery introduces the SignedGeneSet class, directly extending GeneSet from the GSEABase package.  To increase performance of large queries, multiple gene sets are stored as sparse incidence matrices within CMAPCollection eSets. gCMAP offers implementations of 1.  Fisher's exact test (Fisher, J R Stat Soc, 1922) 2. The \"connectivity map\" method (Lamb et al, Science, 2006) 3. Parametric and non-parametric t-statistic summaries (Jiang & Gentleman, Bioinformatics, 2007) and 4. Wilcoxon / Mann-Whitney rank sum statistics (Wilcoxon, Biometrics Bulletin, 1945) as well as wrappers for the 5. camera (Wu & Smyth, Nucleic Acid Res, 2012) 6. mroast and romer (Wu et al, Bioinformatics, 2010) functions from the limma package. All methods return CMAPResult objects, an S4 class inheriting from AnnotatedDataFrame, containing enrichment statistics as well as annotation data and providing simple high-level summary plots.",
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    "vignetteTitles": [
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    "URL": "http://www.ibe.med.uni-muenchen.de",
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    "Title": "Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays",
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      "biomaRt",
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    "Maintainer": "Steffen Durinck <sdurinck@gmail.com>",
    "Author": "Steffen Durinck <sdurinck@gmail.com>, James Bullard <bullard@berkeley.edu>",
    "Title": "Plotting genomic information from Ensembl",
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    "vignettes": [
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    "License": "Artistic-2.0",
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    "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.",
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    "win.binary.ver": "bin/windows/contrib/2.16/GenomeGraphs_1.19.0.zip"
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      "ChemmineR",
      "methods"
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    "hasNEWS": true,
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    "URL": "http://manuals.bioinformatics.ucr.edu/home/chemminer",
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    "Title": "Flexible Maximum Common Substructure (FMCS) Searching",
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    "NeedsCompilation": "yes",
    "Package": "fmcsR",
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    "Archs": "i386, x64",
    "License": "Artistic-2.0",
    "hasREADME": false,
    "biocViews": [
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      "Clustering",
      "DataImport",
      "Infrastructure",
      "MicrotitrePlateAssay",
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      "Visualization"
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    "Description": "The fmcsR package introduces an efficient maximum common substructure (MCS) algorithms combined with a novel matching strategy that allows for atom and/or bond mismatches in the substructures shared among two small molecules. The resulting flexible MCSs (FMCSs) are often larger than strict MCSs, resulting in the identification of more common features in their source structures, as well as a higher sensitivity in finding compounds with weak structural similarities. The fmcsR package provides several utilities to use the FMCS algorithm for pairwise compound comparisons, structure similarity searching and clustering.",
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    "win.binary.ver": "bin/windows/contrib/2.16/fmcsR_1.1.0.zip"
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      "BiocGenerics",
      "Biobase"
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    "win64.binary.ver": "bin/windows64/contrib/2.16/tigre_1.13.1.zip",
    "hasNEWS": true,
    "mac.binary.leopard.ver": "bin/macosx/leopard/contrib/2.16/tigre_1.13.1.tgz",
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    "hasINSTALL": false,
    "MD5sum": "b827ee27a708f61630816109341b82ed",
    "URL": "http://www.bioinf.manchester.ac.uk/resources/tiger/",
    "Maintainer": "Antti Honkela <antti.honkela@hiit.fi>",
    "Author": "Antti Honkela, Pei Gao, Jonatan Ropponen, Miika-Petteri Matikainen, Magnus Rattray, Neil D. Lawrence",
    "Title": "Transcription factor Inference through Gaussian process Reconstruction of Expression",
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    "Imports": [
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      "annotate",
      "DBI",
      "RSQLite"
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    "NeedsCompilation": "yes",
    "Suggests": [
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    "Package": "tigre",
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    "Archs": "i386, x64",
    "License": "AGPL-3",
    "hasREADME": false,
    "biocViews": [
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      "Software",
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    "Description": "The tigre package implements our methodology of Gaussian process differential equation models for analysis of gene expression time series from single input motif networks. The package can be used for inferring unobserved transcription factor (TF) protein concentrations from expression measurements of known target genes, or for ranking candidate targets of a TF.",
    "hasLICENSE": false,
    "win.binary.ver": "bin/windows/contrib/2.16/tigre_1.13.1.zip"
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    "Depends": [
      "limma",
      "MASS",
      "R(>= 2.10)",
      "Biobase",
      "methods"
    ],
    "vignetteTitles": [
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    "Maintainer": "Benedikt Zacher <zacher@lmb.uni-muenchen.de>",
    "Author": "Benedikt Zacher, Khalid Abnaof, Stephan Gade, Erfan Younesi, Achim Tresch, Holger Froehlich",
    "Title": "Bayesian Inference of Regulation of Transcriptional Activity",
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    "NeedsCompilation": "yes",
    "Package": "birta",
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    "Description": "Expression levels of mRNA molecules are regulated by different processes, comprising inhibition or activation by transcription factors and post-transcriptional degradation by microRNAs. birta (Bayesian Inference of Regulation of Transcriptional Activity) uses the regulatory networks of TFs and miRNAs together with mRNA and miRNA expression data to predict switches in regulatory activity between two conditions. A Bayesian network is used to model the regulatory structure and Markov-Chain-Monte-Carlo is applied to sample the activity states.",
    "hasLICENSE": false,
    "win.binary.ver": "bin/windows/contrib/2.16/birta_1.3.0.zip"
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  "Rgraphviz": {
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      "methods",
      "utils",
      "graph",
      "grid"
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    "vignetteTitles": [
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    "hasNEWS": true,
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    "MD5sum": "cb1ee9a19ab53299977aa8d4093f346e",
    "Maintainer": "Kasper Daniel Hansen <khansen@jhsph.edu>",
    "Author": "Jeff Gentry, Li Long, Robert Gentleman, Seth Falcon, Florian Hahne, Deepayan Sarkar, Kasper Daniel Hansen",
    "Title": "Provides plotting capabilities for R graph objects",
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      "flowMerge",
      "GeneNetworkBuilder",
      "geneplotter",
      "GlobalAncova",
      "globaltest",
      "GOstats",
      "GSEABase",
      "GSVA",
      "KEGGgraph",
      "MLP",
      "NCIgraph",
      "NCIgraphData",
      "oneChannelGUI",
      "pcaGoPromoter",
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      "Rtreemix",
      "safe",
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      "Streamer",
      "topGO"
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    "biocViews": [
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    "Description": "Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package. Users on all platforms must install graphviz; see the README file, available in the source distribution of this file, for details.",
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    ],
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    "URL": "http://research.jax.org/faculty/churchill",
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    "Author": "Hao Wu, modified by Hyuna Yang and Keith Sheppard with ideas from Gary Churchill, Katie Kerr and Xiangqin Cui.",
    "Title": "Tools for analyzing Micro Array experiments",
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    "biocViews": [
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    "Description": "Analysis of N-dye Micro Array experiment using mixed model effect. Containing analysis of variance, permutation and bootstrap, cluster and consensus tree.",
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      "fields",
      "Biobase"
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    "Author": "Claudio Isella",
    "Title": "Calculates Mulcom test",
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    "Imports": [
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    "Archs": "i386, x64",
    "License": "GPL-2",
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    "biocViews": [
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      "locfit",
      "tkrplot",
      "methods"
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    "Maintainer": "IFC Development Team <info-genarise@ifc.unam.mx>",
    "Author": "Ana Patricia Gomez Mayen <pgomez@ifc.unam.mx>,\\\\ Gustavo Corral Guille <gcorral@ifc.unam.mx>, \\\\ Lina Riego Ruiz <lriego@ifc.unam.mx>,\\\\ Gerardo Coello Coutino <gcoello@ifc.unam.mx>",
    "Title": "Microarray Analysis tool",
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    "Imports": [
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      "methods",
      "stats",
      "tcltk",
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      "xtable"
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    "NeedsCompilation": "no",
    "Package": "genArise",
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    "License": "file LICENSE",
    "hasREADME": false,
    "biocViews": [
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    "Description": "genArise is an easy to use tool for dual color microarray data. Its GUI-Tk based environment let any non-experienced user performs a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer.",
    "hasLICENSE": true,
    "win.binary.ver": "bin/windows/contrib/2.16/genArise_1.35.0.zip"
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      "DNAcopy",
      "methods"
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    "vignetteTitles": [
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    "win64.binary.ver": "bin/windows64/contrib/2.16/snapCGH_1.29.0.zip",
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    "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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      "GLAD",
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      "utils"
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    "NeedsCompilation": "yes",
    "Package": "snapCGH",
    "vignettes": [
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    "Archs": "i386, x64",
    "License": "GPL",
    "hasREADME": false,
    "biocViews": [
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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.",
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    "win.binary.ver": "bin/windows/contrib/2.16/snapCGH_1.29.0.zip"
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    "vignetteTitles": [
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    "Maintainer": "Lihua Julie Zhu <julie.zhu@umassmed.edu>",
    "Author": "Lihua Julie Zhu, Herve Pages, Claude Gazin, Nathan Lawson, Jianhong Ou, Simon Lin, David Lapointe and Michael Green",
    "Title": "Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges.",
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    "Title": "A graphical user interface to conduct a dose-response analysis of microarray data",
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    "Maintainer": "Tobias Verbeke <tobias.verbeke@openanalytics.eu>",
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      "methods"
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    "Title": "A normalization method for Copy Number Aberration in cancer samples",
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    "Imports": [
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    "NeedsCompilation": "yes",
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    "Author": "K. Myriam Kroll, Fabrice Berger, Gerard Barkema, Enrico Carlon",
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    "Description": "affyILM is a preprocessing tool which estimates gene expression levels for Affymetrix Gene Chips. Input from physical chemistry is employed to first background subtract intensities before calculating concentrations on behalf of the Langmuir model.",
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    "Author": "David Henriques, Thomas Cokelaer",
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    "Package": "CNORode",
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    "vignetteTitles": [
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    "Imports": [
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      "methods"
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    "NeedsCompilation": "yes",
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    "Package": "DirichletMultinomial",
    "vignettes": [
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    "Archs": "i386, x64",
    "License": "LGPL-3",
    "hasREADME": false,
    "biocViews": [
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      "HighThroughputSequencing",
      "Software"
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    "SystemRequirements": "gsl",
    "win.binary.ver": "bin/windows/contrib/2.16/DirichletMultinomial_1.1.0.zip"
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    "hasNEWS": true,
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    "Description": "Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.",
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      "stats",
      "RColorBrewer",
      "Biobase",
      "methods",
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    "biocViews": [
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    "NeedsCompilation": "no",
    "Suggests": [
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    "win.binary.ver": "bin/windows/contrib/2.16/RefPlus_1.29.0.zip"
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    "hasINSTALL": false,
    "MD5sum": "75255988fee1fb6ae9ddda498c8fe7db",
    "Maintainer": "Bioconductor Package Maintainer <maintainer@bioconductor.org>",
    "Author": "Herve Pages, Marc Carlson, Seth Falcon, Nianhua Li",
    "Title": "Annotation Database Interface",
    "suggestsMe": [
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    "NeedsCompilation": "no",
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      "vignettes/AnnotationDbi/inst/doc/databaseTypes.pdf",
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    "License": "Artistic-2.0",
    "hasREADME": false,
    "biocViews": [
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    "Description": "Provides user interface and database connection code for annotation data packages using SQLite data storage.",
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      "IRanges",
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    "Title": "de novo motif discovery",
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    "Maintainer": "Zhenpeng Li<zpli21@gmail.com>",
    "Author": "Zhenpeng Li, Yang Huang, Yabo Ouyang, Liying Ma",
    "Title": "Detect the correlated mutations based on selection pressure",
    "source.ver": "src/contrib/CorMut_1.1.0.tar.gz",
    "NeedsCompilation": "no",
    "Package": "CorMut",
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