https://github.com/dessimozlab/omadb
https://github.com/dessimozlab/omadb
Last synced: 24 days ago
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- Host: GitHub
- URL: https://github.com/dessimozlab/omadb
- Owner: DessimozLab
- License: gpl-3.0
- Created: 2018-12-01T12:28:23.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2024-04-18T06:09:45.000Z (almost 2 years ago)
- Last Synced: 2026-02-05T11:18:13.019Z (about 1 month ago)
- Language: Jupyter Notebook
- Size: 436 KB
- Stars: 2
- Watchers: 4
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS
- License: LICENSE.md
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README
# 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.
[](https://mybinder.org/v2/gh/DessimozLab/omadb/master?filepath=manuscript_examples.ipynb)
## 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.17548.2)_
## 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.
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 .