SeqGSEA (version 1.8.1)

SeqGSEA-package: SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data

Description

SeqGSEA is an R package for gene set enrichment analysis of RNA-Seq data with the ability to integrate differential expression and differential splice in functional analysis.

Details

Package:

SeqGSEA

Type:

Package

License:

GPL (>= 3)

A User's Guide is available as well as the usual help page documentation for each of the individual functions.

The most useful functions are listed below:

* ReadCountSet class

• ReadCountSet-class
• ReadCountSet
• exonID
• geneID
• counts-methods
• label
• subsetByGenes

* SeqGeneSet class

• SeqGeneSet-class
• geneSetDescs
• geneSetNames
• geneSetSize
• size

* Load data

• newReadCountSet
• loadExonCountData
• newGeneSets
• loadGenesets

* DE analysis

• getGeneCount
• runDESeq
• DENBStat4GSEA
• DENBStatPermut4GSEA
• DENBTest
• DEpermutePval

* DS analysis

• DSpermute4GSEA
• DSpermutePval
• exonTestability
• geneTestability
• estiExonNBstat
• estiGeneNBstat

* GSEA main

• GSEnrichAnalyze
• calES
• calES.perm
• genePermuteScore
• geneScore
• rankCombine
• normES
• normFactor
• scoreNormalization
• signifES

* Result tables

• GSEAresultTable
• DSresultExonTable
• DSresultGeneTable
• topDEGenes
• topDSExons
• topDSGenes
• topGeneSets

* Result displays

• plotES
• plotGeneScore
• plotSig
• plotSigGeneSet
• writeSigGeneSet

* Miscellaneous

• genpermuteMat
• convertEnsembl2Symbol
• convertSymbol2Ensembl

References

Xi Wang and Murray J. Cairns (2013). Gene Set Enrichment Analysis of RNA-Seq Data: Integrating Differential Expression and Splicing. BMC Bioinformatics, 14(Suppl 5):S16.