orthogene
This is thereleased version of orthogene; for the devel version, seeorthogene.
Interspecies gene mapping
Bioconductor version: Release (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.
Author: Brian Schilder [cre]
ORCID: 0000-0001-5949-2191
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")BiocManager::install("orthogene")For older versions of R, please refer to the appropriateBioconductor 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 | 1.16.0 |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | orthogene_1.16.0.tar.gz |
| Windows Binary (x86_64) | orthogene_1.16.0.zip |
| macOS Binary (x86_64) | orthogene_1.16.0.tgz |
| macOS Binary (arm64) | orthogene_1.16.0.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 |
| Old Source Packages for BioC 3.22 | Source Archive |