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pairedGSEA

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

Paired DGE and DGS analysis for gene set enrichment analysis


Bioconductor version: Development (3.19)

pairedGSEA makes it simple to run a paired Differential Gene Expression (DGE) and Differencital Gene Splicing (DGS) analysis. The package allows you to store intermediate results for further investiation, if desired. pairedGSEA comes with a wrapper function for running an Over-Representation Analysis (ORA) and functionalities for plotting the results.

Author: Søren Helweg Dam [cre, aut] , Lars Rønn Olsen [aut] , Kristoffer Vitting-Seerup [aut]

Maintainer: Søren Helweg Dam <sohdam at dtu.dk>

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

Installation

To install this package, start R (version "4.4") and enter:


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

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

BiocManager::install("pairedGSEA")

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("pairedGSEA")
User Guide HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, GeneSetEnrichment, ImmunoOncology, Pathways, RNASeq, Software, Transcription
Version 1.3.1
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License MIT + file LICENSE
Depends R (>= 4.3.0)
Imports DESeq2, DEXSeq, limma, fgsea, sva, SummarizedExperiment, S4Vectors, BiocParallel, ggplot2, aggregation, stats, utils, methods
System Requirements
URL https://github.com/shdam/pairedGSEA
Bug Reports https://github.com/shdam/pairedGSEA/issues
See More
Suggests writexl, readxl, readr, rhdf5, msigdbr, plotly, testthat (>= 3.0.0), knitr, rmarkdown, covr, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
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Build Report Build Report

Package Archives

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

Source Package pairedGSEA_1.3.1.tar.gz
Windows Binary pairedGSEA_1.3.1.zip
macOS Binary (x86_64) pairedGSEA_1.3.1.tgz
macOS Binary (arm64) pairedGSEA_1.3.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/pairedGSEA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/pairedGSEA
Bioc Package Browser https://code.bioconductor.org/browse/pairedGSEA/
Package Short Url https://bioconductor.org/packages/pairedGSEA/
Package Downloads Report Download Stats