SeqGSEA-package: SeqGSEA: a Bioconductor package for gene set enrichment...

In SeqGSEA: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

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

Author(s)

Xi Wang and Murray J. Cairns

Maintainer: Xi Wang <[e-mail]>

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.

SeqGSEA documentation built on Nov. 8, 2020, 5:46 p.m.