orthogene

DOI: 10.18129/B9.bioc.orthogene    

Interspecies gene mapping

Bioconductor version: Release (3.16)

`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]

Maintainer: Brian Schilder <brian_schilder at alumni.brown.edu>

Citation (from within R, enter citation("orthogene")):

Installation

To install this package, start R (version "4.2") 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")

 

HTML R Script docker
HTML R Script Infer species
HTML R Script orthogene
PDF   Reference Manual
Text   NEWS

Details

biocViews ComparativeGenomics, GeneExpression, Genetics, Phylogenetics, Preprocessing, Software, Transcriptomics
Version 1.4.1
In Bioconductor since BioC 3.14 (R-4.1) (1 year)
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
LinkingTo
Suggests remotes, knitr, BiocStyle, covr, markdown, rmarkdown, here, testthat (>= 3.0.0), piggyback, badger, magick, desc, hrbrthemes, Cairo, yulab.utils, haven, GenomeInfoDbData, ape, phytools, rphylopic, TreeTools, RColorBrewer, ggimage, OmaDB
SystemRequirements
Enhances
URL https://github.com/neurogenomics/orthogene
BugReports https://github.com/neurogenomics/orthogene/issues
Depends On Me
Imports Me EWCE
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package orthogene_1.4.1.tar.gz
Windows Binary orthogene_1.4.1.zip
macOS Binary (x86_64) orthogene_1.4.1.tgz
macOS Binary (arm64) orthogene_1.4.1.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 3.16 Source Archive

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