This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

orthogene

Interspecies gene mapping

Bioconductor version: Release (3.17)

`orthogene` is an R package for easy mapping of orthologous genes across hundreds of species. It pulls up-to-date gene ortholog mappings across **700+ organisms**. It also provides various utility functions to aggregate/expand common objects (e.g. data.frames, gene expression matrices, lists) using **1:1**, **many:1**, **1:many** or **many:many** gene mappings, both within- and between-species.

Author: Brian Schilder [cre]

Maintainer: Brian Schilder <brian_schilder at alumni.brown.edu>

Citation (from within R, enter citation("orthogene")):

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("orthogene")

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("orthogene")
docker HTML R Script
Infer species HTML R Script
orthogene HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ComparativeGenomics, GeneExpression, Genetics, Phylogenetics, Preprocessing, Software, Transcriptomics
Version 1.6.1
In Bioconductor since BioC 3.14 (R-4.1) (2 years)
License GPL-3
Depends R (>= 4.1)
Imports dplyr, methods, stats, utils, Matrix, jsonlite, homologene, gprofiler2, babelgene, data.table, parallel, ggplot2, ggpubr, patchwork, DelayedArray, grr, repmis, ggtree, tools
Linking To
Suggests rworkflows, remotes, knitr, BiocStyle, markdown, rmarkdown, testthat (>= 3.0.0), piggyback, magick, GenomeInfoDbData, ape, phytools, rphylopic (>= 1.0.0), TreeTools, ggimage, OmaDB
System Requirements
Enhances
URL https://github.com/neurogenomics/orthogene
Bug Reports https://github.com/neurogenomics/orthogene/issues
See More
Depends On Me
Imports Me EWCE
Suggests Me MACP
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package orthogene_1.6.1.tar.gz
Windows Binary orthogene_1.6.1.zip (64-bit only)
macOS Binary (x86_64) orthogene_1.6.1.tgz
macOS Binary (arm64) orthogene_1.6.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/orthogene
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/orthogene
Bioc Package Browser https://code.bioconductor.org/browse/orthogene/
Package Short Url https://bioconductor.org/packages/orthogene/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.17 Source Archive