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orthogene

Gene mapping made easy

Bioconductor version: 3.23 · Package version: 1.18.1

`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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("orthogene")

Details

MaintainerBrian Schilder <brian_schilder@alumni.brown.edu>
AuthorBrian Schilder [cre, fnd] (ORCID: <https://orcid.org/0000-0001-5949-2191>)
LicenseGPL-3
URLhttps://github.com/neurogenomics/orthogene
Bug Reportshttps://github.com/neurogenomics/orthogene/issues
Downloads rank880
Source branchRELEASE_3_23
biocViewsComparativeGenomics, GeneExpression, Genetics, Phylogenetics, Preprocessing, Software, Transcriptomics

Documentation

Download

Dependencies

Depends: R (>= 4.5.0)

Imports: dplyr, methods, stats, utils, Matrix, jsonlite, homologene, gprofiler2, babelgene, data.table, parallel, ggplot2, ggpubr, patchwork, DelayedArray, repmis, ggtree, tools, magrittr

Suggests: remotes, knitr, BiocStyle, markdown, rmarkdown, testthat (>= 3.0.0), piggyback, magick, GenomeInfoDbData, ape, phytools, rphylopic (>= 1.0.0), TreeTools, ggimage, OmaDB

Reverse dependencies

Imports Me (2): BulkSignalR, EWCE

Suggests Me (1): sparrow