DOI: 10.18129/B9.bioc.SeqGSEA  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see SeqGSEA.

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

Bioconductor version: 3.16

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 at>

Maintainer: Xi Wang <Xi.Wang at>

Citation (from within R, enter citation("SeqGSEA")):


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PDF R Script Gene set enrichment analysis of RNA-Seq data with the SeqGSEA package
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biocViews DifferentialExpression, DifferentialSplicing, GeneExpression, GeneSetEnrichment, ImmunoOncology, RNASeq, Sequencing, Software
Version 1.38.0
In Bioconductor since BioC 2.12 (R-3.0) (10 years)
License GPL (>= 3)
Depends Biobase, doParallel, DESeq2
Imports methods, biomaRt
Suggests GenomicRanges
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