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

The package generally provides methods for gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing. It uses negative binomial distribution to model read count data, which accounts for sequencing biases and biological variation. Based on permutation tests, statistical significance can also be achieved regarding each gene's differential expression and splicing, respectively.

AuthorXi Wang <Xi.Wang@newcastle.edu.au>
Date of publicationNone
MaintainerXi Wang <Xi.Wang@mdc-berlin.de>
LicenseGPL (>= 3)
Version1.14.0

View on Bioconductor

Man pages

calES: Calculate running enrichment scores of gene sets

calES.perm: Calculate enrichment scores for gene sets in the permutation...

convertEnsembl2Symbol: Convert ensembl gene IDs to gene symbols

convertSymbol2Ensembl: Convert gene symbols to ensembl gene IDs

counts-methods: Accessors for the 'counts' slot of a ReadCountSet object.

DENBStat4GSEA: Calculate NB-statistics quantifying differential expression...

DENBStatPermut4GSEA: Calculate NB-statistics quantifying DE for each gene in the...

DENBTest: Perform negative binomial exact test for differential...

DEpermutePval: Permutation for p-values in differential expression analysis

DEscore: Pre-calculated DE/DS scores

DSpermute4GSEA: Compute NB-statistics quantifying differential splicing on...

DSpermutePval: Permutation for p-values in differential splicing analysis

DSresultExonTable: Form a table for DS analysis results at the Exon level

DSresultGeneTable: Form a table for DS analysis results at the gene level

estiExonNBstat: Calculate NB-statistics quantifying differential splicing for...

estiGeneNBstat: Calculate NB-statistics quantifying differential splicing for...

exonID: Accessor to the exonID slot of ReadCountSet objects

exonTestability: Check exon testability

geneID: Accessor to the geneID slot of ReadCountSet objects

geneList: Get the gene list in a SeqGeneSet object

genePermuteScore: Calculate gene scores on permutation data sets

geneScore: Calculate gene scores by integrating DE and DS scores

geneSetDescs: Get the descriptions of gene sets in a SeqGeneSet object

geneSetNames: Get the names of gene set in a SeqGeneSet object

geneSetSize: Get the numbers of genes in each gene set in a SeqGeneSet...

geneTestability: Check gene testability

genpermuteMat: Generate permutation matrix

getGeneCount: Calculate read counts of genes from a ReadCountSet object

GSEAresultTable: Form a table for GSEA results

GSEnrichAnalyze: Main function of gene set enrichment analysis

GS_example: SeqGeneSet object example

label: Get the labels of samples in a ReadCountSet object

loadExonCountData: Load Exon Count Data

loadGenesets: Load gene sets from files

newGeneSets: Initialize a new SeqGeneSet object

newReadCountSet: Generate a new ReadCountSet object

normES: Normalize enrichment scores

normFactor: Get normalization factors for normalization DE or DS scores

plotES: Plot the distribution of enrichment scores

plotGeneScore: Plot gene (DE/DS) scores

plotSig: Plot showing SeqGeneSet's p-values/FDRs vs. NESs

plotSigGeneSet: Plot gene set details

rankCombine: Integration of differential expression and differential...

RCS_example: ReadCountSet object example

ReadCountSet-class: Class '"ReadCountSet"'

runDESeq: Run DESeq for differential expression analysis

runSeqGSEA: An all-in function that allows end users to apply SeqGSEA to...

scoreNormalization: Normalization of DE/DS scores

SeqGeneSet-class: Class '"SeqGeneSet"'

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

signifES: Calculate significance of ESs

size: Number of gene sets in a SeqGeneSet object

subsetByGenes: Get a new ReadCountSet with specified gene IDs.

topDEGenes: Extract top differentially expressed genes.

topDSExons: Extract top differentially spliced exons

topDSGenes: Extract top differentially spliced genes

topGeneSets: Extract top significant gene sets

writeScores: Write DE/DS scores and gene scores

writeSigGeneSet: Write gene set supporting information

Functions

calES Man page
calES.perm Man page
convertEnsembl2Symbol Man page
convertSymbol2Ensembl Man page
counts Man page
counts-methods Man page
counts<-,ReadCountSet,matrix-method Man page
counts,ReadCountSet-method Man page
DENBStat4GSEA Man page
DENBStatPermut4GSEA Man page
DENBTest Man page
DEpermutePval Man page
DEscore Man page
DEscore.perm Man page
DSpermute4GSEA Man page
DSpermutePval Man page
DSresultExonTable Man page
DSresultGeneTable Man page
DSscore Man page
DSscore.perm Man page
estiExonNBstat Man page
estiGeneNBstat Man page
exonID Man page
exonID<- Man page
exonTestability Man page
geneID Man page
geneID<- Man page
geneList Man page
genePermuteScore Man page
geneScore Man page
geneSetDescs Man page
geneSetNames Man page
geneSetSize Man page
geneTestability Man page
genpermuteMat Man page
getGeneCount Man page
GSEAresultTable Man page
GSEnrichAnalyze Man page
GS_example Man page
label Man page
loadExonCountData Man page
loadGenesets Man page
newGeneSets Man page
newReadCountSet Man page
normES Man page
normFactor Man page
plotES Man page
plotGeneScore Man page
plotSig Man page
plotSigGeneSet Man page
rankCombine Man page
RCS_example Man page
ReadCountSet Man page
ReadCountSet-class Man page
runDESeq Man page
runSeqGSEA Man page
scoreNormalization Man page
SeqGeneSet Man page
SeqGeneSet-class Man page
[,SeqGeneSet,numeric-method Man page
SeqGSEA Man page
SeqGSEA-package Man page
show,SeqGeneSet-method Man page
signifES Man page
size Man page
subsetByGenes Man page
topDEGenes Man page
topDSExons Man page
topDSGenes Man page
topGeneSets Man page
writeScores Man page
writeSigGeneSet Man page

Files

SeqGSEA/DESCRIPTION
SeqGSEA/NAMESPACE
SeqGSEA/NEWS
SeqGSEA/R
SeqGSEA/R/Allclasses.R SeqGSEA/R/DEscore.R SeqGSEA/R/DSscore.R SeqGSEA/R/SeqGSEA.R SeqGSEA/R/estiNB.R SeqGSEA/R/plots.R
SeqGSEA/build
SeqGSEA/build/vignette.rds
SeqGSEA/data
SeqGSEA/data/DEscore.RData
SeqGSEA/data/DEscore.perm.RData
SeqGSEA/data/DSscore.RData
SeqGSEA/data/DSscore.perm.RData
SeqGSEA/data/GS_example.RData
SeqGSEA/data/RCS_example.RData
SeqGSEA/inst
SeqGSEA/inst/CITATION
SeqGSEA/inst/doc
SeqGSEA/inst/doc/SeqGSEA.R
SeqGSEA/inst/doc/SeqGSEA.Rnw
SeqGSEA/inst/doc/SeqGSEA.pdf
SeqGSEA/inst/extdata
SeqGSEA/inst/extdata/SC02.exonCnt.txt
SeqGSEA/inst/extdata/SC03.exonCnt.txt
SeqGSEA/inst/extdata/SC06.exonCnt.txt
SeqGSEA/inst/extdata/SC08.exonCnt.txt
SeqGSEA/inst/extdata/SC09.exonCnt.txt
SeqGSEA/inst/extdata/SC11.exonCnt.txt
SeqGSEA/inst/extdata/SC13.exonCnt.txt
SeqGSEA/inst/extdata/SC15.exonCnt.txt
SeqGSEA/inst/extdata/SC19.exonCnt.txt
SeqGSEA/inst/extdata/SC23.exonCnt.txt
SeqGSEA/inst/extdata/SN02.exonCnt.txt
SeqGSEA/inst/extdata/SN03.exonCnt.txt
SeqGSEA/inst/extdata/SN06.exonCnt.txt
SeqGSEA/inst/extdata/SN08.exonCnt.txt
SeqGSEA/inst/extdata/SN09.exonCnt.txt
SeqGSEA/inst/extdata/SN11.exonCnt.txt
SeqGSEA/inst/extdata/SN13.exonCnt.txt
SeqGSEA/inst/extdata/SN15.exonCnt.txt
SeqGSEA/inst/extdata/SN19.exonCnt.txt
SeqGSEA/inst/extdata/SN23.exonCnt.txt
SeqGSEA/inst/extdata/geneCounts.txt
SeqGSEA/inst/extdata/gs_symb.txt
SeqGSEA/inst/extscripts
SeqGSEA/inst/extscripts/count_in_exons.py
SeqGSEA/inst/extscripts/prepare_exon_annotation_ensembl.py
SeqGSEA/inst/extscripts/prepare_exon_annotation_refseq.py
SeqGSEA/man
SeqGSEA/man/DENBStat4GSEA.Rd SeqGSEA/man/DENBStatPermut4GSEA.Rd SeqGSEA/man/DENBTest.Rd SeqGSEA/man/DEpermutePval.Rd SeqGSEA/man/DEscore.Rd SeqGSEA/man/DSpermute4GSEA.Rd SeqGSEA/man/DSpermutePval.Rd SeqGSEA/man/DSresultExonTable.Rd SeqGSEA/man/DSresultGeneTable.Rd SeqGSEA/man/GSEAresultTable.Rd SeqGSEA/man/GSEnrichAnalyze.Rd SeqGSEA/man/GS_example.Rd SeqGSEA/man/RCS_example.Rd SeqGSEA/man/ReadCountSet-class.Rd SeqGSEA/man/SeqGSEA-package.Rd SeqGSEA/man/SeqGeneSet-class.Rd SeqGSEA/man/calES.Rd SeqGSEA/man/calES.perm.Rd SeqGSEA/man/convertEnsembl2Symbol.Rd SeqGSEA/man/convertSymbol2Ensembl.Rd SeqGSEA/man/counts-methods.Rd SeqGSEA/man/estiExonNBstat.Rd SeqGSEA/man/estiGeneNBstat.Rd SeqGSEA/man/exonID.Rd SeqGSEA/man/exonTestability.Rd SeqGSEA/man/geneID.Rd SeqGSEA/man/geneList.Rd SeqGSEA/man/genePermuteScore.Rd SeqGSEA/man/geneScore.Rd SeqGSEA/man/geneSetDescs.Rd SeqGSEA/man/geneSetNames.Rd SeqGSEA/man/geneSetSize.Rd SeqGSEA/man/geneTestability.Rd SeqGSEA/man/genpermuteMat.Rd SeqGSEA/man/getGeneCount.Rd SeqGSEA/man/label.Rd SeqGSEA/man/loadExonCountData.Rd SeqGSEA/man/loadGenesets.Rd SeqGSEA/man/newGeneSets.Rd SeqGSEA/man/newReadCountSet.Rd SeqGSEA/man/normES.Rd SeqGSEA/man/normFactor.Rd SeqGSEA/man/plotES.Rd SeqGSEA/man/plotGeneScore.Rd SeqGSEA/man/plotSig.Rd SeqGSEA/man/plotSigGeneSet.Rd SeqGSEA/man/rankCombine.Rd SeqGSEA/man/runDESeq.Rd SeqGSEA/man/runSeqGSEA.Rd SeqGSEA/man/scoreNormalization.Rd SeqGSEA/man/signifES.Rd SeqGSEA/man/size.Rd SeqGSEA/man/subsetByGenes.Rd SeqGSEA/man/topDEGenes.Rd SeqGSEA/man/topDSExons.Rd SeqGSEA/man/topDSGenes.Rd SeqGSEA/man/topGeneSets.Rd SeqGSEA/man/writeScores.Rd SeqGSEA/man/writeSigGeneSet.Rd
SeqGSEA/vignettes
SeqGSEA/vignettes/SeqGSEA.Rnw
SeqGSEA/vignettes/SeqGSEA.bib

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