orthogene

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see orthogene.

Interspecies gene mapping

Bioconductor version: 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")
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ComparativeGenomics, GeneExpression, Genetics, Phylogenetics, Preprocessing, Software, Transcriptomics

Version 1.10.0

In Bioconductor since BioC 3.14 (R-4.1) (3 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

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Package Archives

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

Source Package orthogene_1.10.0.tar.gz

Windows Binary (x86_64) orthogene_1.10.0.zip

macOS Binary (x86_64) orthogene_1.10.0.tgz

macOS Binary (arm64) orthogene_1.10.0.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/

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