Package: HTSanalyzeR
Type: Package
Title: Gene set over-representation, enrichment and network analyses
        for high-throughput screens
Version: 2.18.0
Date: 2013-09-29
Author: Xin Wang <xinwang2hms@gmail.com>, Camille Terfve
        <cdat2@cam.ac.uk>, John C. Rose <jcr53@cam.ac.uk>, Florian
        Markowetz <Florian.Markowetz@cruk.cam.ac.uk>
Maintainer: Xin Wang <xinwang2hms@gmail.com>
Depends: R (>= 2.15), igraph, methods
Imports: graph, igraph, GSEABase, BioNet, cellHTS2, AnnotationDbi,
        biomaRt, RankProd
Suggests: KEGG.db, GO.db, org.Dm.eg.db, GOstats, org.Ce.eg.db,
        org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, snow
Description: This package provides classes and methods for gene set
        over-representation, enrichment and network analyses on
        high-throughput screens. The over-representation analysis is
        performed based on hypergeometric tests. The enrichment
        analysis is based on the GSEA algorithm (Subramanian et al.
        PNAS 2005). The network analysis identifies enriched
        subnetworks based on algorithms from the BioNet package
        (Beisser et al., Bioinformatics 2010). A pipeline is also
        specifically designed for cellHTS2 object to perform
        integrative network analyses of high-throughput RNA
        interference screens. The users can build their own analysis
        pipeline for their own data set based on this package.
Reference: Xin Wang and Camille Terfve and John C. Rose and Florian
        Markowetz. HTSanalyzeR: an R/Bioconductor package for
        integrated network analysis of high-throughput screens.
        Bioinformatics 27:6 879 (2011).
License: Artistic-2.0
Collate: paraCheck.R aggregatePvals.R analyzeGeneSetCollections.R
        annotationConvertor.R biogridDataDownload.R
        celAnnotationConvertor.R cellHTS2OutputStatTests.R
        collectionGsea.R drosoAnnotationConvertor.R duplicateRemover.R
        FDRcollectionGsea.R GOGeneSets.R gseaPlots.R gseaScores.R
        gseaScoresBatch.R gseaScoresBatchParallel.R hyperGeoTest.R
        HTSanalyzeR4cellHTS2.R HTSanalyzeR-internal.R KeggGeneSets.R
        mammalAnnotationConvertor.R multiHyperGeoTest.R
        networkAnalysis.R networkPlot.R classUnions.R AllGenerics.R
        AllClasses.R GSCA-methods.R NWA-methods.R pairwiseGsea.R
        pairwiseGseaPlot.R pairwisePhenoMannWhit.R
        permutationPvalueCollectionGsea.R writeHtml.R writeReportHTSA.R
        zzz.R
LazyLoad: yes
biocViews: CellBasedAssays, MultipleComparison
Packaged: 2014-10-14 01:52:40 UTC; biocbuild
