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")):

Installation

To install this package, start R (version "4.1") 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")

docker HTML R Script

Infer species HTML R Script

orthogene HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ComparativeGenomics, GeneExpression, Genetics, Phylogenetics, Preprocessing, Software, Transcriptomics

Version 1.0.2

In Bioconductor since BioC 3.14 (R-4.1) (2.5 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, DelayedMatrixStats, Matrix.utils, grr, repmis, GenomeInfoDbData, tools

System Requirements

URL https://github.com/neurogenomics/orthogene

Bug Reports https://github.com/neurogenomics/orthogene/issues

Suggests remotes, knitr, BiocStyle, covr, markdown, rmarkdown, here, testthat (>= 3.0.0), piggyback, badger, magick

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