Phenotype

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<!-- PROJECT LOGO --> <br /> <p align="center"> <a href="https://github.com/glasgowm148/Phenotype"> <img src="https://github.com/glasgowm148/Phenotype/blob/master/docs/img/logo.png" alt="Logo"> </a> <h3 align="center">Phenotype</h3> <p align="center"> Genomic Analysis <br /> <a href="https://github.com/glasgowm148/Phenotype/tree/main/Phenotype/data/docs"><strong>Explore the docs »</strong></a> <br /> <br /> <a href="https://github.com/glasgowm148/Phenotype/data/demo">View Demo</a> · <a href="https://github.com/glasgowm148/Phenotype/issues">Report Bug</a> · <a href="https://github.com/glasgowm148/Phenotype/issues">Request Feature</a> </p> </p> <!-- TABLE OF CONTENTS --> <details open="open"> <summary><h2 style="display: inline-block">Table of Contents</h2></summary> <ol> <li> <a href="#about-the-project">About The Project</a> <ul> <li><a href="#built-with">Built With</a></li> </ul> </li> <li> <a href="#getting-started">Getting Started</a> <ul> <li><a href="#prerequisites">Prerequisites</a></li> <li><a href="#installation">Installation</a></li> </ul> </li> <li><a href="#usage">Usage</a></li> <li><a href="#roadmap">Roadmap</a></li> <li><a href="#contributing">Contributing</a></li> <li><a href="#license">License</a></li> <li><a href="#contact">Contact</a></li> <li><a href="#acknowledgements">Acknowledgements</a></li> </ol> </details> <!-- ABOUT THE PROJECT -->

About The Project

Phenotype is an open source web application that allows users to gather the information they need to make sense of their own genome without needing to rely on outside services with unknown privacy policies. OS Genome's goal is to crawl various sources and give meaning to an individual's genome. It creates a Responsive Grid of the user's specific genome. This allows for everything from filtering to excel exporting. Using Flask, Kendo, and Python.

Jupyter-playground

Various notebooks used to explore SNP data. The two main files currently retrieve 500-1k rsids a second using MyVariant.info which returns XML

Currently exports a plain HTML table, NaN and 23andme i-rsid's dropped and sorted by adviser rating.

• Scrape & Save queries your rsids against ClinVar and returns assosciations, risk allele's, frequency - and stores it in a datatable.
• Load & Analyse matches your rsids against the ClinVar dataframe pulled from Scrape & Save. This can be exported to CSV or HTML.

Limitations

Currently only tested with 23andme V4 & V5.

ToDo

• Beautify HTML datatable using DataTables
• Flatten all DTC file formats into a consistent dataframe for manipulation
• Add more sources of data
  • SNPedia
  • ONIM
• Data-validaiton
  • strand orientation
  • risk allelle debugging

<!-- GETTING STARTED ## Getting Started ### Installation <!-- USAGE EXAMPLES ## Overview <!-- ROADMAP ## Roadmap See the [open issues](https://github.com/glasgowm148/Phenotype/issues) for a list of proposed features (and known issues). <!-- CONTRIBUTING -->

Contributing

Contributions are what make the open source community such an amazing place to be learn, inspire, and create. Any contributions you make are greatly appreciated.

1. Fork the Project
2. Create your Feature Branch (git checkout -b feature/AmazingFeature)
3. Commit your Changes (git commit -m 'Add some AmazingFeature')
4. Push to the Branch (git push origin feature/AmazingFeature)
5. Open a Pull Request

<!-- LICENSE -->

License

Distributed under the MIT License. See LICENSE for more information.

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Contact

Mark Glasgow - markglasgow@gmail.com

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Acknowledgements

• OSGenome
• SNPApi,
• Snappy

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