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

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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.

Author
Xi Wang <Xi.Wang@newcastle.edu.au>
Date of publication
None
Maintainer
Xi Wang <Xi.Wang@mdc-berlin.de>
License
GPL (>= 3)
Version
1.14.0

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

Files in this package

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