topGO
This is the development version of topGO; for the stable release version, see topGO.
Enrichment Analysis for Gene Ontology
Bioconductor version: Development (3.22)
topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.
Author: Adrian Alexa [aut], Jörg Rahnenführer [aut], Federico Marini [cre]
Maintainer: Federico Marini <marinif at uni-mainz.de>
citation("topGO")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("topGO")
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("topGO")| Gene set enrichment analysis with topGO | HTML | R Script |
| Reference Manual |
Details
| biocViews | Annotation, GO, GeneExpression, GeneSetEnrichment, Microarray, Pathways, Sequencing, Software, SystemsBiology, Transcriptomics, Visualization |
| Version | 2.61.1 |
| In Bioconductor since | BioC 2.0 (R-2.5) (18.5 years) |
| License | LGPL |
| Depends | R (>= 2.10.0), methods, BiocGenerics(>= 0.13.6), graph(>= 1.14.0), Biobase(>= 2.0.0), GO.db(>= 2.3.0), AnnotationDbi(>= 1.7.19), SparseM (>= 0.73) |
| Imports | lattice, matrixStats, DBI |
| System Requirements | |
| URL | https://github.com/federicomarini/topGO |
| Bug Reports | https://github.com/federicomarini/topGO/issues |
See More
| Suggests | ALL, hgu95av2.db, hgu133a.db, genefilter, multtest, Rgraphviz, globaltest, knitr, BiocStyle, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | BgeeDB, compEpiTools, EGSEA, ideal, moanin, tRanslatome, maEndToEnd |
| Imports Me | APL, cellity, consICA, GRaNIE, mosdef, OmaDB, pcaExplorer, transcriptogramer, ViSEAGO, ExpHunterSuite |
| Suggests Me | DeeDeeExperiment, fenr, FGNet, GeDi, geva, IntramiRExploreR, miRNAtap |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | topGO_2.61.1.tar.gz |
| Windows Binary (x86_64) | topGO_2.61.1.zip (64-bit only) |
| macOS Binary (x86_64) | topGO_2.61.1.tgz |
| macOS Binary (arm64) | topGO_2.61.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/topGO |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/topGO |
| Bioc Package Browser | https://code.bioconductor.org/browse/topGO/ |
| Package Short Url | https://bioconductor.org/packages/topGO/ |
| Package Downloads Report | Download Stats |