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Bioconductor - pairedGSEA

pairedGSEA

This is the released version of pairedGSEA; for the devel version, see pairedGSEA.

Paired DGE and DGS analysis for gene set enrichment analysis

Bioconductor version: Release (3.21)

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] ORCID: 0000-0002-9895-0930 , Lars Rønn Olsen [aut] ORCID: 0000-0002-6725-7850 , Kristoffer Vitting-Seerup [aut] ORCID: 0000-0002-6450-0608

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

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

To install this package, start R (version "4.5") and enter:


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

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")
Details biocViews AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, GeneSetEnrichment, ImmunoOncology, Pathways, RNASeq, Software, Transcription Version 1.8.0 In Bioconductor since BioC 3.17 (R-4.3) (2 years) License MIT + file LICENSE Depends R (>= 4.4.0) Imports DESeq2, DEXSeq, limma, fgsea, msigdbr, sva, SummarizedExperiment, S4Vectors, BiocParallel, ggplot2, aggregation, stats, utils, methods, showtext System Requirements URL https://github.com/shdam/pairedGSEA Bug Reports https://github.com/shdam/pairedGSEA/issues See More Package Archives

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

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