https://github.com/stuntspt/pyrona

A python implementation of "Risk of non Adaptedness" method (with a bit of R too!)
https://github.com/stuntspt/pyrona

Last synced: 4 months ago
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A python implementation of "Risk of non Adaptedness" method (with a bit of R too!)

• Host: GitHub
• URL: https://github.com/stuntspt/pyrona
• Owner: StuntsPT
• License: gpl-3.0
• Created: 2016-11-11T21:59:48.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2021-08-02T16:52:44.000Z (over 4 years ago)
• Last Synced: 2025-02-02T04:41:13.496Z (about 1 year ago)
• Language: Python
• Homepage:
• Size: 1.51 MB
• Stars: 11
• Watchers: 5
• Forks: 3
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE

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README

          
# pyRona

A python implementation of "Risk of non Adaptedness" method (with a bit of R too!)

[![Build Status](https://travis-ci.org/StuntsPT/pyRona.svg?branch=master)](https://travis-ci.org/StuntsPT/pyRona) [![Documentation Status](https://readthedocs.org/projects/pyrona/badge/?version=latest)](http://pyrona.readthedocs.io/en/latest/?badge=latest) [![PyPI version](https://badge.fury.io/py/pyRona.svg)](https://badge.fury.io/py/pyRona) [![DOI](https://zenodo.org/badge/73514698.svg)](https://zenodo.org/badge/latestdoi/73514698)

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## pyRona manual

*pyRona* is not yet fully documented, but you can find the manual [here](http://pyrona.readthedocs.io/en/latest/).

## Baypass_workflow.R

If you came here looking for a way to automate the *BayPass* analysis, you should be especially interested in it's [manual section](http://pyrona.readthedocs.io/en/latest/baypass/). You can find the script [here](https://gitlab.com/StuntsPT/pyRona/blob/master/pyRona/R/Baypass_workflow.R).

## LFMM and LFMM2 helper scripts

If you came here looking for a way to automate *LFMM*/*LFMM2* analysws, you should be especially interested in it's [manual section](http://pyrona.readthedocs.io/en/latest/lfmm/). You can find the scripts for both *LFMM* and *LFMM2* [here](https://gitlab.com/StuntsPT/pyRona/blob/master/pyRona/R/).

## Installation

Installing *pyRona* can be as simple as typing `pip3 install pyRona` from the command line. For more information, and platform specific instructions, please consult the [relevant manual section](http://pyrona.readthedocs.io/en/latest/install/).

## Citation

If you use `pyRona` please cite our ~~pre-print: [New insights on adaptation and population structure of cork oak using genotyping by sequencing](https://doi.org/10.1101/263160)~~ paper: [New insights into adaptation and population structure of cork oak using genotyping by sequencing](https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.14497)

## License

*pyRona* is licensed under the [GNU GPLv3](https://www.gnu.org/licenses/gpl-3.0-standalone.html).