SeqGSEA-package {SeqGSEA} | R Documentation

## 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`

### 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.

[Package SeqGSEA version 1.30.0 Index]