toppgene

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.

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
Downloads rank	109
Source branch	devel
biocViews	Clustering, GeneExpression, GeneSetEnrichment, Genetics, MotifDiscovery, Network, NetworkEnrichment, Pathways, Pharmacogenetics, Proteomics, Software, ThirdPartyClient

Documentation

Exporatory data analysis by querying the ToppGene Suite

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)