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OmaDB

This is the development version of OmaDB; for the stable release version, see OmaDB.

R wrapper for the OMA REST API


Bioconductor version: Development (3.20)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
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 HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, ComparativeGenomics, FunctionalGenomics, FunctionalPrediction, GO, Genetics, Software
Version 2.21.0
In Bioconductor since BioC 3.7 (R-3.5) (6 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
System Requirements
URL https://github.com/DessimozLab/OmaDB
Bug Reports https://github.com/DessimozLab/OmaDB/issues
See More
Suggests knitr, rmarkdown, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me orthogene, PhyloProfile
Links To Me
Build Report Build Report

Package Archives

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

Source Package OmaDB_2.21.0.tar.gz
Windows Binary OmaDB_2.21.0.zip
macOS Binary (x86_64) OmaDB_2.21.0.tgz
macOS Binary (arm64) OmaDB_2.21.0.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