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

## Documentation for package ‘SeqGSEA’ version 1.40.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

SeqGSEA-package | SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data
calES | Calculate running enrichment scores of gene sets
calES.perm | Calculate enrichment scores for gene sets in the permutation data sets
convertEnsembl2Symbol | Convert ensembl gene IDs to gene symbols
convertSymbol2Ensembl | Convert gene symbols to ensembl gene IDs
counts | Accessors for the 'counts' slot of a ReadCountSet object.
counts-method | Accessors for the 'counts' slot of a ReadCountSet object.
counts-methods | Accessors for the 'counts' slot of a ReadCountSet object.
counts<--method | Accessors for the 'counts' slot of a ReadCountSet object.
DENBStat4GSEA | Calculate NB-statistics quantifying differential expression for each gene
DENBStatPermut4GSEA | Calculate NB-statistics quantifying DE for each gene in the permutation data sets
DENBTest | Perform negative binomial exact test for differential expression
DEpermutePval | Permutation for p-values in differential expression analysis
DEscore | Pre-calculated DE/DS scores
DEscore.perm | Pre-calculated DE/DS scores
DSpermute4GSEA | Compute NB-statistics quantifying differential splicing on the permutation data set.
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
DSscore | Pre-calculated DE/DS scores
DSscore.perm | Pre-calculated DE/DS scores
estiExonNBstat | Calculate NB-statistics quantifying differential splicing for individual exons
estiGeneNBstat | Calculate NB-statistics quantifying differential splicing for each gene
exonID | Accessor to the exonID slot of ReadCountSet objects
exonID<- | Accessor to the exonID slot of ReadCountSet objects
exonTestability | Check exon testability
geneID | Accessor to the geneID slot of ReadCountSet objects
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 object
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 splice scores with a rank-based strategy
RCS_example | ReadCountSet object example
ReadCountSet | Class '"ReadCountSet"'
ReadCountSet-class | Class '"ReadCountSet"'
runDESeq | Run DESeq for differential expression analysis
runSeqGSEA | An all-in function that allows end users to apply SeqGSEA to their data with one step.
scoreNormalization | Normalization of DE/DS scores
SeqGeneSet | Class '"SeqGeneSet"'
SeqGeneSet-class | Class '"SeqGeneSet"'
SeqGSEA | SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data
show-method | Class '"SeqGeneSet"'
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
[-method | Class '"SeqGeneSet"'