Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

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 |

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