OmaDB

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see OmaDB.

R wrapper for the OMA REST API


Bioconductor version: 3.9

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 "3.6") 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")
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 2.0.0
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
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Build Report Build Report

Package Archives

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

Source Package OmaDB_2.0.0.tar.gz
Windows Binary OmaDB_2.0.0.zip
Mac OS X 10.11 (El Capitan) OmaDB_2.0.0.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 3.9 Source Archive