This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

pairedGSEA

Paired DGE and DGS analysis for gene set enrichment analysis

Bioconductor version: Release (3.17)

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")

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 1.0.0
In Bioconductor since BioC 3.17 (R-4.3) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.2.0)
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
Links To Me
Build Report  

Package Archives

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

Source Package pairedGSEA_1.0.0.tar.gz
Windows Binary pairedGSEA_1.0.0.zip
macOS Binary (x86_64) pairedGSEA_1.0.0.tgz
macOS Binary (arm64) pairedGSEA_1.0.0.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