DOI: 10.18129/B9.bioc.orthogene  

This is the development version of orthogene; for the stable release version, see orthogene.

Interspecies gene mapping

Bioconductor version: Development (3.19)

`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")):


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biocViews ComparativeGenomics, GeneExpression, Genetics, Phylogenetics, Preprocessing, Software, Transcriptomics
Version 1.9.0
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
Suggests rworkflows, remotes, knitr, BiocStyle, markdown, rmarkdown, testthat (>= 3.0.0), piggyback, magick, GenomeInfoDbData, ape, phytools, rphylopic (>= 1.0.0), TreeTools, ggimage, OmaDB
URL https://github.com/neurogenomics/orthogene
BugReports https://github.com/neurogenomics/orthogene/issues
Depends On Me
Imports Me EWCE
Suggests Me MACP
Links To Me
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Package Archives

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

Source Package orthogene_1.9.0.tar.gz
Windows Binary orthogene_1.9.0.zip
macOS Binary (x86_64) orthogene_1.9.0.tgz
macOS Binary (arm64)
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/
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