toppgene
This is the development version of toppgene; to use it, please install the devel version of Bioconductor.
Gene List Enrichment Analysis using the ToppGene Suite
Bioconductor version: Development (3.23)
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("toppgene")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("toppgene")
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("toppgene")| toppgene | HTML | R Script |
| Reference Manual |
Details
| biocViews | Clustering, GeneExpression, GeneSetEnrichment, Genetics, MotifDiscovery, Network, NetworkEnrichment, Pathways, Pharmacogenetics, Proteomics, Software, ThirdPartyClient |
| Version | 0.99.1 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | GPL (>= 3) |
| Depends | R (>= 4.6.0) |
| Imports | BiocFileCache, httr2, IRanges, jsonlite, methods, purrr, readr, S4Vectors, xml2, yaml |
| System Requirements | |
| URL | https://github.com/ImmunoSystems-lab/toppgene |
| Bug Reports | https://github.com/ImmunoSystems-lab/toppgene/issues |
See More
| Suggests | BiocStyle, DFplyr(>= 1.5.0), knitr, rmarkdown, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| 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 | toppgene_0.99.1.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/toppgene |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/toppgene |
| Bioc Package Browser | https://code.bioconductor.org/browse/toppgene/ |
| Package Short Url | https://bioconductor.org/packages/toppgene/ |
| Package Downloads Report | Download Stats |