ReactomeGSA
This is the released version of ReactomeGSA; for the devel version, see ReactomeGSA.
Client for the Reactome Analysis Service for comparative multi-omics gene set analysis
Bioconductor version: Release (3.23)
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]
Maintainer: Johannes Griss <johannes.griss at meduniwien.ac.at>
citation("ReactomeGSA")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.26.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 years) |
| License | MIT + file LICENSE |
| 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 | |
| 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_1.26.0.tar.gz |
| Windows Binary (x86_64) | ReactomeGSA_1.26.0.zip |
| macOS Binary (big-sur-x86_64) | ReactomeGSA_1.26.0.tgz |
| macOS Binary (sonoma-arm64) | ReactomeGSA_1.26.0.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 3.23 | Source Archive |