DOI: 10.18129/B9.bioc.orthogene    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see orthogene.

Interspecies gene mapping

Bioconductor version: 3.14

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>

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


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biocViews ComparativeGenomics, GeneExpression, Genetics, Phylogenetics, Preprocessing, Software, Transcriptomics
Version 1.0.2
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
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, GenomeInfoDbData, tools
Suggests remotes, knitr, BiocStyle, covr, markdown, rmarkdown, here, testthat (>= 3.0.0), piggyback, badger, magick
URL https://github.com/neurogenomics/orthogene
BugReports https://github.com/neurogenomics/orthogene/issues
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Source Package orthogene_1.0.2.tar.gz
Windows Binary orthogene_1.0.2.zip (32- & 64-bit)
macOS 10.13 (High Sierra) orthogene_1.0.2.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/
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