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ReactomeGSA
This is thereleased version of ReactomeGSA; for the devel version, seeReactomeGSA.
Client for the Reactome Analysis Service for comparative multi-omics gene set analysis
Bioconductor version: Release (3.22)
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: 0000-0003-2206-9511
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")BiocManager::install("ReactomeGSA")For older versions of R, please refer to the appropriateBioconductor 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 | 1.24.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (6 years) |
| License | MIT + fileLICENSE |
| Depends | |
| Imports | Biobase,BiocSingular,dplyr,ggplot2,gplots,httr,igraph,jsonlite, methods,progress,RColorBrewer,SummarizedExperiment,tidyr |
| System Requirements | |
| URL | https://github.com/reactome/ReactomeGSA |
| Bug Reports | https://github.com/reactome/ReactomeGSA/issues |
See More
| Suggests | devtools,knitr,ReactomeGSA.data,rmarkdown,scater,scran,scRNAseq,scuttle,Seurat (>= 3.0),SingleCellExperiment,testthat |
| Linking To | |
| Enhances | |
| Depends On Me | ReactomeGSA.data |
| Imports Me | scPipeline |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | ReactomeGSA_1.24.0.tar.gz |
| Windows Binary (x86_64) | ReactomeGSA_1.24.0.zip |
| macOS Binary (x86_64) | ReactomeGSA_1.24.0.tgz |
| macOS Binary (arm64) | ReactomeGSA_1.24.0.tgz |
| 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 |
| Old Source Packages for BioC 3.22 | Source Archive |