OmaDB

DOI: 10.18129/B9.bioc.OmaDB  

R wrapper for the OMA REST API

Bioconductor version: Release (3.17)

A package for the orthology prediction data download from OMA database.

Author: Klara Kaleb

Maintainer: Klara Kaleb <klara.kaleb18 at ic.ac.uk>, Adrian Altenhoff <adrian.altenhoff at inf.ethz.ch>

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

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("OmaDB")

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("OmaDB")

 

HTML R Script Exploring Hierarchical orthologous groups with OmaDB
HTML R Script Exploring Taxonomic trees with OmaDB
HTML R Script Get started with OmaDB
HTML R Script Sequence Mapping with OmaDB
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, ComparativeGenomics, FunctionalGenomics, FunctionalPrediction, GO, Genetics, Software
Version 2.16.0
In Bioconductor since BioC 3.7 (R-3.5) (5.5 years)
License GPL-3
Depends R (>= 3.5), httr (>= 1.2.1), plyr (>= 1.8.4)
Imports utils, ape, Biostrings, GenomicRanges, IRanges, methods, topGO, jsonlite
LinkingTo
Suggests knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL https://github.com/DessimozLab/OmaDB
BugReports https://github.com/DessimozLab/OmaDB/issues
Depends On Me
Imports Me PhyloProfile
Suggests Me orthogene
Links To Me
Build Report  

Package Archives

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

Source Package OmaDB_2.16.0.tar.gz
Windows Binary OmaDB_2.16.0.zip
macOS Binary (x86_64) OmaDB_2.16.0.tgz
macOS Binary (arm64) OmaDB_2.16.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/OmaDB
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/OmaDB
Bioc Package Browser https://code.bioconductor.org/browse/OmaDB/
Package Short Url https://bioconductor.org/packages/OmaDB/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.17 Source Archive

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: