orthogene
This is the development version of orthogene; for the stable release version, see orthogene.
Interspecies gene mapping
Bioconductor version: Development (3.22)
`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")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text |
Details
| biocViews | ComparativeGenomics, GeneExpression, Genetics, Phylogenetics, Preprocessing, Software, Transcriptomics |
| Version | 1.15.02 |
| In Bioconductor since | BioC 3.14 (R-4.1) (4 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 | BulkSignalR, EWCE |
| Suggests Me | sparrow |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | orthogene_1.15.02.tar.gz |
| Windows Binary (x86_64) | orthogene_1.15.0.zip |
| macOS Binary (x86_64) | orthogene_1.15.02.tgz |
| macOS Binary (arm64) | orthogene_1.15.02.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 |