HTSanalyzeR : Gene set over-representation, enrichment and network analyses for high-throughput screens

Package: HTSanalyzeR
Type: Package
Title: Gene set over-representation, enrichment and network analyses
for high-throughput screens
Version: 2.24.0
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
NeedsCompilation: no
Packaged: 2016-05-04 03:53:32 UTC; biocbuild