orthogene
Interspecies gene mapping
Bioconductor version: Release (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.
Maintainer: Brian Schilder <brian_schilder at alumni.brown.edu>
citation("orthogene")
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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 | ||
NEWS | Text |
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 |
See More
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 | |
Enhances | |
Depends On Me | |
Imports Me | EWCE |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | orthogene_1.10.0.tar.gz |
Windows Binary | 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/ |
Package Downloads Report | Download Stats |