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)|
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