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"' |