- SeqGSEA: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
- normES: Normalize enrichment scores
Normalize enrichment scores
This is an internal function to normalize enrichment scores. For advanced users only.
a SeqGeneSet object after running
A SeqGeneSet object with ES scores normalized.
Xi Wang, email@example.com
Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.
- 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