Last data update: 2014.03.03

HTSanalyzeR

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

● BiocViews: CellBasedAssays, MultipleComparison
● 0 images, 53 functions, 1 datasets
● Reverse Depends: 0

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'HTSanalyzeR' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
** help
*** installing help indices
  converting help for package 'HTSanalyzeR'
    finding HTML links ... done
    FDRcollectionGsea                       html  
    GOGeneSets                              html  
    GSCA-class                              html  
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/GSCA-class.Rd:112: missing file link 'writeHits'
    GenHTSAHtmlRowUnit                      html  
    HTSanalyzeR                             html  
    HTSanalyzeR4cellHTS2                    html  
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/HTSanalyzeR4cellHTS2.Rd:8: missing file link 'GSCA'
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/HTSanalyzeR4cellHTS2.Rd:9: missing file link 'NWA'
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/HTSanalyzeR4cellHTS2.Rd:207: missing file link 'GSCA'
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/HTSanalyzeR4cellHTS2.Rd:218: missing file link 'GSCA'
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/HTSanalyzeR4cellHTS2.Rd:218: missing file link 'NWA'
    KeggGeneSets                            html  
    NWA-class                               html  
    aggregatePvals                          html  
    analyze                                 html  
    analyzeGeneSetCollections               html  
    annotationConvertor                     html  
    appendGSTerms                           html  
    biogridDataDownload                     html  
    celAnnotationConvertor                  html  
    cellHTS2OutputStatTests                 html  
    changes                                 html  
    collectionGsea                          html  
    data-KcViab                             html  
    drosoAnnotationConvertor                html  
    duplicateRemover                        html  
    getTopGeneSets                          html  
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/getTopGeneSets.Rd:10: missing file link 'GSCA'
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/getTopGeneSets.Rd:18: missing file link 'GSCA'
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    gseaPlots                               html  
    gseaScores                              html  
    htmlAttrVectorPaste                     html  
    hyperGeoTest                            html  
    interactome                             html  
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    makeGSEAplots                           html  
    makeOverlapTable                        html  
    mammalAnnotationConvertor               html  
    multiHyperGeoTest                       html  
    networkAnalysis                         html  
    networkPlot                             html  
    pairwiseGsea                            html  
    pairwiseGseaPlot                        html  
    pairwisePhenoMannWhit                   html  
    paraCheck                               html  
    permutationPvalueCollectionGsea         html  
    plotEnrichMap                           html  
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/plotEnrichMap.Rd:10: missing file link 'GSCA'
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    plotGSEA                                html  
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/plotGSEA.Rd:10: missing file link 'GSCA'
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Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/plotGSEA.Rd:29: missing file link 'GSCA'
    plotSubNet                              html  
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/plotSubNet.Rd:10: missing file link 'NWA'
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    preprocess                              html  
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/preprocess.Rd:11: missing file link 'GSCA'
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Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/preprocess.Rd:35: missing file link 'NWA'
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/preprocess.Rd:112: missing file link 'GSCA'
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/preprocess.Rd:113: missing file link 'NWA'
    report                                  html  
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/report.Rd:11: missing file link 'GSCA'
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/report.Rd:11: missing file link 'NWA'
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/report.Rd:15: missing file link 'GSCA'
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/report.Rd:15: missing file link 'NWA'
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/report.Rd:25: missing file link 'GSCA'
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/report.Rd:25: missing file link 'NWA'
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/report.Rd:26: missing file link 'GSCA'
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/report.Rd:26: missing file link 'NWA'
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/report.Rd:30: missing file link 'GSCA'
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/report.Rd:30: missing file link 'NWA'
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/report.Rd:69: missing file link 'GSCA'
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    reportAll                               html  
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/reportAll.Rd:10: missing file link 'GSCA'
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/reportAll.Rd:10: missing file link 'NWA'
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/reportAll.Rd:14: missing file link 'GSCA'
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/reportAll.Rd:14: missing file link 'NWA'
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/reportAll.Rd:24: missing file link 'GSCA'
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    summarize                               html  
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/summarize.Rd:14: missing file link 'GSCA'
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    viewEnrichMap                           html  
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    viewGSEA                                html  
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    viewSubNet                              html  
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    writeHTSAHtmlHead                       html  
    writeHTSAHtmlSummary                    html  
    writeHTSAHtmlTab                        html  
    writeHTSAHtmlTable                      html  
    writeHTSAHtmlTail                       html  
    writeReportHTSA                         html  
Rd warning: /tmp/RtmpTVipjv/R.INSTALL5d642e54ca9d/HTSanalyzeR/man/writeReportHTSA.Rd:8: missing file link 'GSCA'
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** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
* DONE (HTSanalyzeR)
Making 'packages.html' ... done

Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO