orthogene

DOI: 10.18129/B9.bioc.orthogene    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see orthogene.

Interspecies gene mapping

Bioconductor version: 3.15

orthogene is an R package for easy mapping of orthologous genes across hundreds of species. It pulls up-to-date interspecies gene ortholog mappings across 700+ organisms. It also provides various utility functions to map common objects (e.g. data.frames, gene expression matrices, lists) onto 1:1 gene orthologs from any other species.

Author: Brian Schilder [cre]

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

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	1.2.1
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, DelayedMatrixStats, Matrix.utils, 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
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_1.2.1.tar.gz
Windows Binary	orthogene_1.2.1.zip
macOS Binary (x86_64)	orthogene_1.2.1.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