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README.md

OmaDB: R wrapper for the OMA REST API

R package providing access to the data in the OMA browser, using the REST API. As such, it requires a stable internet connection to operate. We also provide a similar wrapper for python (https://github.com/DessimozLab/pyOmaDB).

An notebook containing examples of how to use the package is available here.

Binder

Citation

If you use our package in your work, please consider citing:

Kaleb K, Warwick Vesztrocy A, Altenhoff A and Dessimoz C. Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python. F1000Research 2019, 8:42 (https://doi.org/10.12688/f1000research.17548.1)

Installation

The package is available via Bioconductor (https://bioconductor.org) and can be installed as follows:

if (!requireNamespace("BiocManager"))
    install.packages("BiocManager")
BiocManager::install('OmaDB')

#load the package
library(OmaDB)

Note that the v2.0 of the package requires R version >= 3.6 and Bioconductor version >=3.9. At the time of writting this, this is the Bioconductor development version and so the package can be installed as follows:

BiocManager::install('OmaDB', version = 'devel')

Alternatively, the latest version of the OmaDB package can also be directly installed from the github repository as below:

install.packages('devtools')
library(devtools)
install_github('dessimozlab/omadb')

License

OmaDB is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

OmaDB is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. You should have received a copy of the GNU Lesser General Public License along with OmaDB. If not, see http://www.gnu.org/licenses/.

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