orthogene
This is the released version of orthogene; for the devel version, see orthogene.
Gene mapping made easy
Bioconductor version: Release (3.23)
`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, fnd] 
Maintainer: Brian Schilder <brian_schilder at alumni.brown.edu>
citation("orthogene")):Brian Schilder. orthogene: Gene mapping made easy. doi:10.18129/B9.bioc.orthogene, R package version 1.18.1, https://bioconductor.org/packages/orthogene.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text |
Details
| biocViews | ComparativeGenomics, GeneExpression, Genetics, Phylogenetics, Preprocessing, Software, Transcriptomics |
| Version | 1.18.1 |
| In Bioconductor since | BioC 3.14 (R-4.1) (5 years) |
| License | GPL-3 |
| Depends | R (>= 4.5.0) |
| Imports | dplyr, methods, stats, utils, Matrix, jsonlite, homologene, gprofiler2, babelgene, data.table, parallel, ggplot2, ggpubr, patchwork, DelayedArray, repmis, ggtree, tools, magrittr |
| System Requirements | |
| URL | https://github.com/neurogenomics/orthogene |
| Bug Reports | https://github.com/neurogenomics/orthogene/issues |
See More
| Suggests | remotes, knitr, BiocStyle, markdown, rmarkdown, testthat (>= 3.0.0), piggyback, magick, GenomeInfoDbData, ape, phytools, rphylopic (>= 1.0.0), TreeTools, ggimage, OmaDB |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | BulkSignalR, EWCE |
| Suggests Me | sparrow |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | orthogene_1.18.1.tar.gz |
| Windows Binary (x86_64) | orthogene_1.18.1.zip |
| macOS Binary (big-sur-x86_64) | orthogene_1.18.1.tgz |
| macOS Binary (sonoma-arm64) | orthogene_1.18.1.tgz |
| 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 |
| Old Source Packages for BioC 3.23 | Source Archive |