toppgene
This is the development version of toppgene; for the stable release version, see toppgene.
All Bioconductor versions of toppgene
3.24 (devel), 3.23 (release)
Gene List Enrichment Analysis using the ToppGene Suite
Bioconductor version: 3.24 · Package version: 1.1.3
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.
Author: Pariksheet Nanda [aut, cre] 
, Jason Shoemaker [fnd]
Maintainer: Pariksheet Nanda <pan79 at pitt.edu>
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.
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("toppgene")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.1.3 |
| License | GPL (>= 3) |
| URL | https://github.com/ImmuSystems-lab/toppgene |
| Bug Reports | https://github.com/ImmuSystems-lab/toppgene/issues |
| Last updated | 2026-08-03 |
| In Bioconductor since | BioC 3.23 (R-4.6) (less than a year) |
| Downloads rank | 2366 of 2,456 |
| 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/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("toppgene")| Exporatory data analysis by querying the ToppGene Suite | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
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 |
| Source Repository | git clone https://git.bioconductor.org/packages/toppgene |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/toppgene |
| Package Downloads Report | Download Stats |
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)