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Showing content from https://www.bioconductor.org/packages/devel/bioc/html/../html/SeqGSEA.html below:

Bioconductor - SeqGSEA (development version)

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 (3.22)

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 "4.5") 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 1.49.0 In Bioconductor since BioC 2.12 (R-3.0) (12.5 years) License GPL (>= 3) Depends Biobase, doParallel, DESeq2 Imports methods, biomaRt System Requirements URL See More Package Archives

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

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