pairedGSEA
Paired DGE and DGS analysis for gene set enrichment analysis
Bioconductor version: Release (3.20)
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("pairedGSEA")
):
Installation
To install this package, start R (version "4.4") 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 | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, GeneSetEnrichment, ImmunoOncology, Pathways, RNASeq, Software, Transcription |
Version | 1.6.0 |
In Bioconductor since | BioC 3.17 (R-4.3) (1.5 years) |
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 |
See More
Suggests | writexl, readxl, readr, rhdf5, msigdbr, plotly, testthat (>= 3.0.0), knitr, rmarkdown, covr, BiocStyle |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | pairedGSEA_1.6.0.tar.gz |
Windows Binary (x86_64) | pairedGSEA_1.6.0.zip |
macOS Binary (x86_64) | pairedGSEA_1.6.0.tgz |
macOS Binary (arm64) | pairedGSEA_1.5.0.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 |