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

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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 <xi.wang@newcastle.edu.au>

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.

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