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 |
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"' |