toppgene
Gene List Enrichment Analysis using the ToppGene Suite
Bioconductor version: 3.24 · Package version: 1.1.3
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
The ToppGene Suite is a one-stop portal for gene list enrichment analysis and candidate gene prioritization based on functional annotations and protein interactions network. Although the ToppCluster web application provides convenient graphical access to the ToppGene Suite, the OpenAPI 3.0 compliant interface of ToppGene is better suited for automation and reproducibility. This package includes Bioconductor class interfaces and biological examples.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("toppgene")Details
| Maintainer | Pariksheet Nanda <pan79@pitt.edu> |
| Author | Pariksheet Nanda [aut, cre] (ORCID: <https://orcid.org/0000-0001-9726-4552>), Jason Shoemaker [fnd] (ORCID: <https://orcid.org/0000-0003-3315-7103>) |
| License | GPL (>= 3) |
| URL | https://github.com/ImmuSystems-lab/toppgene |
| Bug Reports | https://github.com/ImmuSystems-lab/toppgene/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Clustering, GeneExpression, GeneSetEnrichment, Genetics, MotifDiscovery, Network, NetworkEnrichment, Pathways, Pharmacogenetics, Proteomics, Software, ThirdPartyClient |
| Package Short Url | https://bioconductor.org/packages/toppgene/ |
Citation
From within R, enter citation("toppgene"):
Pariksheet Nanda. toppgene: Gene List Enrichment Analysis using the ToppGene Suite. doi:10.18129/B9.bioc.toppgene, R package version 1.1.3, https://bioconductor.org/packages/toppgene.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | toppgene_1.1.3.tar.gz |
| macOS binary (x86_64) | toppgene_1.1.3.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: BiocFileCache, httr2, IRanges, jsonlite, methods, purrr, readr, S4Vectors, xml2, yaml
Suggests: BiocStyle, DFplyr (>= 1.5.0), knitr, rmarkdown, testthat (>= 3.0.0)