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")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("orthogene")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ComparativeGenomics, GeneExpression, Genetics, Phylogenetics, Preprocessing, Software, Transcriptomics
Version	1.9.0
In Bioconductor since	BioC 3.14 (R-4.1) (2.5 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
System Requirements
URL	https://github.com/neurogenomics/orthogene
Bug Reports	https://github.com/neurogenomics/orthogene/issues

Suggests	rworkflows, remotes, knitr, BiocStyle, markdown, rmarkdown, testthat (>= 3.0.0), piggyback, magick, GenomeInfoDbData, ape, phytools, rphylopic (>= 1.0.0), TreeTools, ggimage, OmaDB
Linking To
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Imports Me	EWCE
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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
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
Package Short Url	https://bioconductor.org/packages/orthogene/
Package Downloads Report	Download Stats