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Bioconductor - orthogene (development version)

orthogene

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

Interspecies gene mapping

Bioconductor version: Development (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 (from within R, enter citation("orthogene")): Installation

To install this package, start R (version "4.5") 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")
Details biocViews ComparativeGenomics, GeneExpression, Genetics, Phylogenetics, Preprocessing, Software, Transcriptomics Version 1.15.0 In Bioconductor since BioC 3.14 (R-4.1) (3.5 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

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

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