Package: gage
Type: Package
Title: Generally Applicable Gene-set Enrichment for Pathway Analysis
Version: 2.60.0
Date: 2022-08-26
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 (>= 3.5.0)
Imports: graph, KEGGREST, AnnotationDbi, GO.db
Suggests: pathview, gageData, org.Hs.eg.db, hgu133a.db, GSEABase,
        Rsamtools, GenomicAlignments,
        TxDb.Hsapiens.UCSC.hg19.knownGene, DESeq2, edgeR, limma
License: GPL (>=2.0)
URL: https://github.com/datapplab/gage,
        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
Config/pak/sysreqs: libpng-dev libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:05:53 UTC
RemoteUrl: https://github.com/bioc/gage
RemoteRef: RELEASE_3_22
RemoteSha: 9b2c4d095f7c1abac9d9da50645e7cc0eeeec7ae
NeedsCompilation: no
Packaged: 2026-02-23 09:23:06 UTC; root
Built: R 4.5.2; ; 2026-02-23 09:25:33 UTC; windows
