ReactomeGSA
This is the development version of ReactomeGSA; for the stable release version, see ReactomeGSA.
Client for the Reactome Analysis Service for comparative multi-omics gene set analysis
Bioconductor version: Development (3.21)
The ReactomeGSA packages uses Reactome's online analysis service to perform a multi-omics gene set analysis. The main advantage of this package is, that the retrieved results can be visualized using REACTOME's powerful webapplication. Since Reactome's analysis service also uses R to perfrom the actual gene set analysis you will get similar results when using the same packages (such as limma and edgeR) locally. Therefore, if you only require a gene set analysis, different packages are more suited.
Author: Johannes Griss [aut, cre] (ORCID:
Maintainer: Johannes Griss <johannes.griss at meduniwien.ac.at>
citation("ReactomeGSA")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("ReactomeGSA")
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("ReactomeGSA")| Analysing single-cell RNAseq data | HTML | R Script |
| Loading and re-analysing public data through ReactomeGSA | HTML | R Script |
| Using the ReactomeGSA package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, GeneSetEnrichment, Proteomics, Reactome, Software, SystemsBiology, Transcriptomics |
| Version | 1.21.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (5 years) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | jsonlite, httr, progress, ggplot2, methods, gplots, RColorBrewer, dplyr, tidyr, Biobase |
| System Requirements | |
| URL | https://github.com/reactome/ReactomeGSA |
| Bug Reports | https://github.com/reactome/ReactomeGSA/issues |
See More
| Suggests | testthat, knitr, rmarkdown, ReactomeGSA.data, devtools |
| Linking To | |
| Enhances | limma, edgeR, Seurat (>= 3.0), scater |
| Depends On Me | ReactomeGSA.data |
| 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 | ReactomeGSA_1.21.0.tar.gz |
| Windows Binary (x86_64) | ReactomeGSA_1.21.0.zip (64-bit only) |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/ReactomeGSA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ReactomeGSA |
| Bioc Package Browser | https://code.bioconductor.org/browse/ReactomeGSA/ |
| Package Short Url | https://bioconductor.org/packages/ReactomeGSA/ |
| Package Downloads Report | Download Stats |