SeqGSEA

DOI: 10.18129/B9.bioc.SeqGSEA    

This package is for version 3.9 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: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	DifferentialExpression, DifferentialSplicing, GeneExpression, GeneSetEnrichment, ImmunoOncology, RNASeq, Sequencing, Software
Version	1.24.0
In Bioconductor since	BioC 2.12 (R-3.0) (6.5 years)
License	GPL (>= 3)
Depends	Biobase, doParallel, DESeq
Imports	methods, biomaRt
LinkingTo
Suggests	easyRNASeq, GenomicRanges
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	SeqGSEA_1.24.0.tar.gz
Windows Binary	SeqGSEA_1.24.0.zip
Mac OS X 10.11 (El Capitan)	SeqGSEA_1.24.0.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