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SeqGSEA

This is the development version of SeqGSEA; for the stable release version, see SeqGSEA.

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

Bioconductor version: Development (3.18)

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")):

Installation

To install this package, start R (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews DifferentialExpression, DifferentialSplicing, GeneExpression, GeneSetEnrichment, ImmunoOncology, RNASeq, Sequencing, Software
Version 1.41.0
In Bioconductor since BioC 2.12 (R-3.0) (10.5 years)
License GPL (>= 3)
Depends Biobase, doParallel, DESeq2
Imports methods, biomaRt
Linking To
Suggests GenomicRanges
System Requirements
Enhances
URL
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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_1.41.0.tar.gz
Windows Binary SeqGSEA_1.41.0.zip
macOS Binary (x86_64) SeqGSEA_1.41.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/SeqGSEA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SeqGSEA
Bioc Package Browser https://code.bioconductor.org/browse/SeqGSEA/
Package Short Url https://bioconductor.org/packages/SeqGSEA/
Package Downloads Report Download Stats