SeqGSEA: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
Version 1.16.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorXi Wang <Xi.Wang@newcastle.edu.au>
Bioconductor views DifferentialExpression GeneExpression GeneSetEnrichment RNASeq Sequencing
Date of publicationNone
MaintainerXi Wang <Xi.Wang@mdc-berlin.de>
LicenseGPL (>= 3)
Version1.16.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SeqGSEA")

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

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

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/Allclasses.R
R/DEscore.R
R/DSscore.R
R/SeqGSEA.R
R/estiNB.R
R/plots.R
build
build/vignette.rds
data
data/DEscore.RData
data/DEscore.perm.RData
data/DSscore.RData
data/DSscore.perm.RData
data/GS_example.RData
data/RCS_example.RData
inst
inst/CITATION
inst/doc
inst/doc/SeqGSEA.R
inst/doc/SeqGSEA.Rnw
inst/doc/SeqGSEA.pdf
inst/extdata
inst/extdata/SC02.exonCnt.txt
inst/extdata/SC03.exonCnt.txt
inst/extdata/SC06.exonCnt.txt
inst/extdata/SC08.exonCnt.txt
inst/extdata/SC09.exonCnt.txt
inst/extdata/SC11.exonCnt.txt
inst/extdata/SC13.exonCnt.txt
inst/extdata/SC15.exonCnt.txt
inst/extdata/SC19.exonCnt.txt
inst/extdata/SC23.exonCnt.txt
inst/extdata/SN02.exonCnt.txt
inst/extdata/SN03.exonCnt.txt
inst/extdata/SN06.exonCnt.txt
inst/extdata/SN08.exonCnt.txt
inst/extdata/SN09.exonCnt.txt
inst/extdata/SN11.exonCnt.txt
inst/extdata/SN13.exonCnt.txt
inst/extdata/SN15.exonCnt.txt
inst/extdata/SN19.exonCnt.txt
inst/extdata/SN23.exonCnt.txt
inst/extdata/geneCounts.txt
inst/extdata/gs_symb.txt
inst/extscripts
inst/extscripts/count_in_exons.py
inst/extscripts/prepare_exon_annotation_ensembl.py
inst/extscripts/prepare_exon_annotation_refseq.py
man
man/DENBStat4GSEA.Rd
man/DENBStatPermut4GSEA.Rd
man/DENBTest.Rd
man/DEpermutePval.Rd
man/DEscore.Rd
man/DSpermute4GSEA.Rd
man/DSpermutePval.Rd
man/DSresultExonTable.Rd
man/DSresultGeneTable.Rd
man/GSEAresultTable.Rd
man/GSEnrichAnalyze.Rd
man/GS_example.Rd
man/RCS_example.Rd
man/ReadCountSet-class.Rd
man/SeqGSEA-package.Rd
man/SeqGeneSet-class.Rd
man/calES.Rd
man/calES.perm.Rd
man/convertEnsembl2Symbol.Rd
man/convertSymbol2Ensembl.Rd
man/counts-methods.Rd
man/estiExonNBstat.Rd
man/estiGeneNBstat.Rd
man/exonID.Rd
man/exonTestability.Rd
man/geneID.Rd
man/geneList.Rd
man/genePermuteScore.Rd
man/geneScore.Rd
man/geneSetDescs.Rd
man/geneSetNames.Rd
man/geneSetSize.Rd
man/geneTestability.Rd
man/genpermuteMat.Rd
man/getGeneCount.Rd
man/label.Rd
man/loadExonCountData.Rd
man/loadGenesets.Rd
man/newGeneSets.Rd
man/newReadCountSet.Rd
man/normES.Rd
man/normFactor.Rd
man/plotES.Rd
man/plotGeneScore.Rd
man/plotSig.Rd
man/plotSigGeneSet.Rd
man/rankCombine.Rd
man/runDESeq.Rd
man/runSeqGSEA.Rd
man/scoreNormalization.Rd
man/signifES.Rd
man/size.Rd
man/subsetByGenes.Rd
man/topDEGenes.Rd
man/topDSExons.Rd
man/topDSGenes.Rd
man/topGeneSets.Rd
man/writeScores.Rd
man/writeSigGeneSet.Rd
vignettes
vignettes/SeqGSEA.Rnw
vignettes/SeqGSEA.bib
SeqGSEA documentation built on May 20, 2017, 10:46 p.m.