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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 (3.18)

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")

# 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 2.17.0
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
Linking To
Suggests knitr, rmarkdown, testthat
System Requirements
Enhances
URL https://github.com/DessimozLab/OmaDB
Bug Reports https://github.com/DessimozLab/OmaDB/issues
See More
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_2.17.0.tar.gz
Windows Binary OmaDB_2.17.0.zip
macOS Binary (x86_64) OmaDB_2.17.0.tgz
macOS Binary (arm64) OmaDB_2.17.0.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