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 (3.22)
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 "4.5") 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 | ||
| NEWS | Text |
Details
| biocViews | Annotation, ComparativeGenomics, FunctionalGenomics, FunctionalPrediction, GO, Genetics, Software |
| Version | 2.25.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (7.5 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 |
| 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_2.25.0.tar.gz |
| Windows Binary (x86_64) | OmaDB_2.25.0.zip (64-bit only) |
| macOS Binary (x86_64) | OmaDB_2.25.0.tgz |
| macOS Binary (arm64) | OmaDB_2.25.0.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 |