OmaDB-package: OmaDB: A package for the orthology prediction data download...

In klarakaleb/OmaDB: R wrapper for the OMA REST API

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

Description

OmaDB is a wrapper for the REST API for the Orthologous MAtrix project (OMA) which is a database for the inference of orthologs among complete genomes. For more details on the OMA project, see https://omabrowser.org/.

OmaDB functions

The package contains a range of functions that are used to query the database. Some of the main functions are listed below:

• getProtein()

• getHOG()

• getOMAGroup()

• getGenomePairs()

• getTaxonomy()

• mapSequence()

• annotateSequence()

• searchProtein()

In addition to these, OmaDB features a range of functions that are used to format the retrieved data into some commonly used Bioconductor objects using packages such as GenomicRanges, Biostrings, topGO and ggtree. Some of them are listed below:

• formatTopGO()

• getGRanges()

The above functions are described in more detail in the package vignette's listed below:

• Get started with OmaDB

• Exploring Hierarchical orthologous groups with OmaDB

• Exploring Taxonomic trees with OmaDB

• Sequence Analysis with OmaDB

klarakaleb/OmaDB documentation built on April 18, 2024, 8:03 a.m.