gage

Package: gage
Type: Package
Title: Generally Applicable Gene-set Enrichment for Pathway Analysis
Version: 2.22.0
Date: 2016-02-18
Author: Weijun Luo
Maintainer: Weijun Luo <luo_weijun@yahoo.com>
Description: GAGE is a published method for gene set (enrichment or GSEA) or pathway analysis. GAGE is generally applicable independent of microarray or RNA-Seq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity, and consistently achieves superior performance over other frequently used methods. In gage package, we provide functions for basic GAGE analysis, result processing and presentation. We have also built pipeline routines for of multiple GAGE analyses in a batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources/studies. In addition, we provide demo microarray data and commonly used gene set data based on KEGG pathways and GO terms. These funtions and data are also useful for gene set analysis using other methods.
biocViews: Pathways, GO, DifferentialExpression, Microarray,
OneChannel, TwoChannel, RNASeq, Genetics, MultipleComparison,
GeneSetEnrichment, GeneExpression, SystemsBiology, Sequencing
Depends: R (>= 2.10)
Imports: graph, KEGGREST, AnnotationDbi
Suggests: pathview, gageData, GO.db, org.Hs.eg.db, hgu133a.db,
GSEABase, Rsamtools, GenomicAlignments,
TxDb.Hsapiens.UCSC.hg19.knownGene, DESeq, DESeq2, edgeR, limma
License: GPL (>=2.0)
URL: http://www.biomedcentral.com/1471-2105/10/161
Collate: colorpanel.R deComp.R eg2sym.R esset.grp.R essGene.R
gageComp.R gage-internal.R gagePipe.R gagePrep.R gage.R
gageSum.R geneData.R go.gsets.R greenred.R gs.heatmap.R
gs.KSTest.R gs.tTest.R gs.zTest.R heatmap2.R heter.gage.R
invalid.R kegg.gsets.R kegg.species.code.R odd.R pairData.R
readExpData.R readList.R rownorm.R sigGeneSet.R sym2eg.R
vennCounts.R vennDiagram2.R
LazyLoad: yes
NeedsCompilation: no
Packaged: 2016-05-04 03:48:08 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'gage' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'gage'
    finding HTML links ... done
    eg2sym                                  html  
    egSymb                                  html  
    essGene                                 html  
    esset.grp                               html  
    gage-internal                           html  
    gage                                    html  
    gageComp                                html  
    gagePipe                                html  
    geneData                                html  
    go.gsets                                html  
    gs.tTest                                html  
    gse16873                                html  
    heter.gage                              html  
    kegg.gs                                 html  
    kegg.gsets                              html  
    readExpData                             html  
    readList                                html  
    sigGeneSet                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gage)
Making 'packages.html' ... done