orthogene
Gene mapping made easy
Bioconductor version: 3.24 · Package version: 1.19.3
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
`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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("orthogene")Details
| Maintainer | Brian Schilder <brian_schilder@alumni.brown.edu> |
| Author | Brian Schilder [cre, fnd] (ORCID: <https://orcid.org/0000-0001-5949-2191>) |
| License | GPL-3 |
| URL | https://github.com/neurogenomics/orthogene |
| Bug Reports | https://github.com/neurogenomics/orthogene/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | ComparativeGenomics, GeneExpression, Genetics, Phylogenetics, Preprocessing, Software, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/orthogene/ |
Citation
From within R, enter citation("orthogene"):
Brian Schilder. orthogene: Gene mapping made easy. doi:10.18129/B9.bioc.orthogene, R package version 1.19.3, https://bioconductor.org/packages/orthogene.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | orthogene_1.19.3.tar.gz |
| Windows binary (x86_64) | orthogene_1.19.3.zip |
| macOS binary (arm64) | orthogene_1.19.3.tgz |
| macOS binary (x86_64) | orthogene_1.19.3.tgz |
Dependencies
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
Suggests: remotes, knitr, BiocStyle, markdown, rmarkdown, testthat (>= 3.0.0), piggyback, magick, GenomeInfoDbData, ape, phytools, rphylopic (>= 1.0.0), TreeTools, ggimage, OmaDB