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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")):


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

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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


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

User Guide HTML R Script
Reference Manual PDF


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
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Suggests writexl, readxl, readr, rhdf5, msigdbr, plotly, testthat (>= 3.0.0), knitr, rmarkdown, covr, BiocStyle
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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/
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