orthogene

DOI: 10.18129/B9.bioc.orthogene  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see orthogene.

Interspecies gene mapping

Bioconductor version: 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>

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")

 

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

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
LinkingTo
Suggests	rworkflows, remotes, knitr, BiocStyle, markdown, rmarkdown, testthat (>= 3.0.0), piggyback, magick, GenomeInfoDbData, ape, phytools, rphylopic (>= 1.0.0), TreeTools, ggimage, OmaDB
SystemRequirements
Enhances
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
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
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