{"id":16618729,"url":"https://github.com/stuntspt/pyrona","last_synced_at":"2025-10-29T19:31:46.362Z","repository":{"id":144924146,"uuid":"73514698","full_name":"StuntsPT/pyRona","owner":"StuntsPT","description":"A python implementation of \"Risk of non Adaptedness\" method (with a bit of R too!)","archived":false,"fork":false,"pushed_at":"2021-08-02T16:52:44.000Z","size":1587,"stargazers_count":11,"open_issues_count":3,"forks_count":3,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-02-02T04:41:13.496Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/StuntsPT.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2016-11-11T21:59:48.000Z","updated_at":"2024-07-28T14:36:40.000Z","dependencies_parsed_at":"2023-07-21T18:38:31.070Z","dependency_job_id":null,"html_url":"https://github.com/StuntsPT/pyRona","commit_stats":null,"previous_names":[],"tags_count":18,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/StuntsPT%2FpyRona","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/StuntsPT%2FpyRona/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/StuntsPT%2FpyRona/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/StuntsPT%2FpyRona/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/StuntsPT","download_url":"https://codeload.github.com/StuntsPT/pyRona/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":238882491,"owners_count":19546529,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-10-12T02:21:20.577Z","updated_at":"2025-10-29T19:31:45.654Z","avatar_url":"https://github.com/StuntsPT.png","language":"Python","readme":"# pyRona\nA python implementation of \"Risk of non Adaptedness\" method (with a bit of R too!)\n\n[![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)\n[![Codacy Badge](https://api.codacy.com/project/badge/Grade/e7952d390d4644d1aae482f94d340695)](https://www.codacy.com/app/f.pinamartins/pyRona?utm_source=github.com\u0026amp;utm_medium=referral\u0026amp;utm_content=StuntsPT/pyRona\u0026amp;utm_campaign=Badge_Grade)\n[![Codacy Badge](https://api.codacy.com/project/badge/Coverage/e7952d390d4644d1aae482f94d340695)](https://www.codacy.com/app/f.pinamartins/pyRona?utm_source=github.com\u0026utm_medium=referral\u0026utm_content=StuntsPT/pyRona\u0026utm_campaign=Badge_Coverage)\n\n\n## pyRona manual\n\n*pyRona* is not yet fully documented, but you can find the manual [here](http://pyrona.readthedocs.io/en/latest/).\n\n\n## Baypass_workflow.R\n\nIf 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).\n\n\n## LFMM and LFMM2 helper scripts\n\nIf 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/).\n\n\n## Installation\n\nInstalling *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/).\n\n\n## Citation\n\nIf 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)\n\n\n## License\n\n*pyRona* is licensed under the [GNU GPLv3](https://www.gnu.org/licenses/gpl-3.0-standalone.html).\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstuntspt%2Fpyrona","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fstuntspt%2Fpyrona","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstuntspt%2Fpyrona/lists"}