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]
, 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 "4.5") 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")| User Guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, GeneSetEnrichment, ImmunoOncology, Pathways, RNASeq, Software, Transcription |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (2.5 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
| Suggests | writexl, readxl, readr, rhdf5, plotly, testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, covr |
| 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_1.8.0.tar.gz |
| Windows Binary (x86_64) | pairedGSEA_1.8.0.zip |
| macOS Binary (x86_64) | pairedGSEA_1.8.0.tgz |
| macOS Binary (arm64) | pairedGSEA_1.8.0.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 |