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orthogene

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

Interspecies gene mapping

Bioconductor version: Development (3.18)

`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")

# 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

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 1.7.0
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
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_1.7.0.tar.gz
Windows Binary orthogene_1.7.1.zip
macOS Binary (x86_64) orthogene_1.7.1.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/
Package Downloads Report Download Stats