pairedGSEA

DOI: 10.18129/B9.bioc.pairedGSEA  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see pairedGSEA.

Paired DGE and DGS analysis for gene set enrichment analysis

Bioconductor version: 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>

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")

 

HTML	R Script	User Guide
PDF		Reference Manual
Text		NEWS
Text		LICENSE

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
LinkingTo
Suggests	writexl, readxl, readr, rhdf5, msigdbr, plotly, testthat (>= 3.0.0), knitr, rmarkdown, covr, BiocStyle
SystemRequirements
Enhances
URL	https://github.com/shdam/pairedGSEA
BugReports	https://github.com/shdam/pairedGSEA/issues
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