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
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
GSEAresultTable         Form a table for GSEA results
GSEnrichAnalyze         Main function of gene set enrichment analysis
GS_example              SeqGeneSet object example
RCS_example             ReadCountSet object example
ReadCountSet-class      Class '"ReadCountSet"'
SeqGSEA-package         SeqGSEA: a Bioconductor package for gene set
                        enrichment analysis of RNA-Seq data
SeqGeneSet-class        Class '"SeqGeneSet"'
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-methods          Accessors for the 'counts' slot of a
                        ReadCountSet object.
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
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 object
geneTestability         Check gene testability
genpermuteMat           Generate permutation matrix
getGeneCount            Calculate read counts of genes from a
                        ReadCountSet object
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
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
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
