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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 (3.18)

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 "4.3") 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

Reference Manual PDF

Details

biocViews AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, GeneSetEnrichment, ImmunoOncology, Pathways, RNASeq, Software, Transcription
Version 1.1.0
In Bioconductor since BioC 3.17 (R-4.3) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.3.0)
Imports DESeq2, DEXSeq, limma, fgsea, sva, SummarizedExperiment, S4Vectors, BiocParallel, ggplot2, aggregation, stats, utils, methods
Linking To
Suggests writexl, readxl, readr, rhdf5, msigdbr, plotly, testthat (>= 3.0.0), knitr, rmarkdown, covr, BiocStyle
System Requirements
Enhances
URL https://github.com/shdam/pairedGSEA
Bug Reports https://github.com/shdam/pairedGSEA/issues
See More
Depends On Me
Imports Me
Suggests Me
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Build Report  

Package Archives

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

Source Package
Windows Binary pairedGSEA_1.1.0.zip
macOS Binary (x86_64) pairedGSEA_1.1.0.tgz
macOS Binary (arm64)
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