pairedGSEA

This is the development version of pairedGSEA; for the stable release version, see pairedGSEA.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17

Paired DGE and DGS analysis for gene set enrichment analysis

Bioconductor version: Development (3.24)

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: Dimitrios S. Kanakoglou [cre, aut], Søren Helweg Dam [aut] ORCID: 0000-0002-9895-0930 , Lars Rønn Olsen [aut] ORCID: 0000-0002-6725-7850 , Kristoffer Vitting-Seerup [aut] ORCID: 0000-0002-6450-0608

Maintainer: Dimitrios S. Kanakoglou <dimkan at dtu.dk>

Citation (from within R, enter citation("pairedGSEA")):

Dimitrios S. Kanakoglou, Søren Helweg Dam, Lars Rønn Olsen, Kristoffer Vitting-Seerup. pairedGSEA: Paired DGE and DGS analysis for gene set enrichment analysis. doi:10.18129/B9.bioc.pairedGSEA, R package version 1.13.0, https://bioconductor.org/packages/pairedGSEA.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, GeneSetEnrichment, ImmunoOncology, Pathways, RNASeq, Software, Transcription
Version	1.13.0
In Bioconductor since	BioC 3.17 (R-4.3) (3.5 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/IsoformAnalysisGroup/pairedGSEA
Bug Reports	https://github.com/IsoformAnalysisGroup/pairedGSEA/issues

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, r-universe

Package Archives

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

Source Package	pairedGSEA_1.13.0.tar.gz
Windows Binary (x86_64)	pairedGSEA_1.13.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	pairedGSEA_1.13.0.tgz
macOS Binary (sonoma-arm64)	pairedGSEA_1.13.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/pairedGSEA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/pairedGSEA
Package Short Url	https://bioconductor.org/packages/pairedGSEA/
Package Downloads Report	Download Stats