orthogene

DOI: 10.18129/B9.bioc.orthogene    

Interspecies gene mapping

Bioconductor version: Release (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 (!requireNamespace("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")

 

HTML R Script Infer species
HTML R Script orthogene
PDF   Reference Manual
Text   NEWS

Details

biocViews ComparativeGenomics, GeneExpression, Genetics, Phylogenetics, Preprocessing, Software, Transcriptomics
Version 1.0.0
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
LinkingTo
Suggests remotes, knitr, BiocStyle, covr, markdown, rmarkdown, here, testthat (>= 3.0.0), piggyback, badger
SystemRequirements
Enhances
URL https://github.com/neurogenomics/orthogene
BugReports https://github.com/neurogenomics/orthogene/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package orthogene_1.0.0.tar.gz
Windows Binary orthogene_1.0.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) orthogene_1.0.0.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
Old Source Packages for BioC 3.14 Source Archive

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