orthogene

DOI: 10.18129/B9.bioc.orthogene    

This is the development version of orthogene; for the stable release version, see orthogene.

Interspecies gene mapping

Bioconductor version: Development (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")

# 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")

 

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 1.3.2
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, 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, 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_1.3.2.tar.gz
Windows Binary orthogene_1.3.2.zip (64-bit only)
macOS Binary (x86_64) orthogene_1.3.2.tgz
macOS Binary (arm64) orthogene_1.3.2.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

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