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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 similarwrapper for python (https://github.com/DessimozLab/pyOmaDB).

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

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.17548.2)

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 packagelibrary(OmaDB)

Note that the v2.0 of the package requires R version >= 3.6 and Bioconductor version >=3.9.

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')

OmaDB is free software: you can redistribute it and/or modifyit under the terms of the GNU Lesser General Public License as published bythe 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 ofMERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See theGNU Lesser General Public License for more details.You should have received a copy of the GNU Lesser General Public Licensealong with OmaDB. If not, seehttp://www.gnu.org/licenses/.