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>

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