SeqGSEA

This is the released version of SeqGSEA; for the devel version, see SeqGSEA.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12

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

Bioconductor version: Release (3.23)

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 newcastle.edu.au>

Maintainer: Xi Wang <Xi.Wang at dkfz.de>

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

Xi Wang. SeqGSEA: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing. doi:10.18129/B9.bioc.SeqGSEA, R package version 1.52.0, https://bioconductor.org/packages/SeqGSEA.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SeqGSEA")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SeqGSEA")

Gene set enrichment analysis of RNA-Seq data with the SeqGSEA package	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, DifferentialSplicing, GeneExpression, GeneSetEnrichment, ImmunoOncology, RNASeq, Sequencing, Software
Version	1.52.0
In Bioconductor since	BioC 2.12 (R-3.0) (13.5 years)
License	GPL (>= 3)
Depends	Biobase, doParallel, DESeq2
Imports	methods, biomaRt
System Requirements
URL

Suggests	GenomicRanges
Linking To
Enhances
Depends On Me
Imports Me
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Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	SeqGSEA_1.52.0.tar.gz
Windows Binary (x86_64)	SeqGSEA_1.52.0.zip
macOS Binary (big-sur-x86_64)	SeqGSEA_1.52.0.tgz
macOS Binary (sonoma-arm64)	SeqGSEA_1.52.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SeqGSEA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SeqGSEA
Package Short Url	https://bioconductor.org/packages/SeqGSEA/
Package Downloads Report	Download Stats