https://github.com/sagar87/genomicsurveillance

https://github.com/sagar87/genomicsurveillance

england epidemiology genomics sars-cov-2 surveillance

Last synced: 3 months ago
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• Host: GitHub
• URL: https://github.com/sagar87/genomicsurveillance
• Owner: sagar87
• License: mit
• Created: 2021-03-03T12:51:48.000Z (over 4 years ago)
• Default Branch: main
• Last Pushed: 2021-10-14T08:02:22.000Z (about 4 years ago)
• Last Synced: 2023-10-24T21:50:23.140Z (almost 2 years ago)
• Topics: england, epidemiology, genomics, sars-cov-2, surveillance
• Language: Jupyter Notebook
• Homepage:
• Size: 1.19 MB
• Stars: 4
• Watchers: 3
• Forks: 6
• Open Issues: 3
• Metadata Files:
  • Readme: README.rst
  • Changelog: HISTORY.rst
  • License: LICENSE

Awesome Lists containing this project

README

          
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Genomic Surveillance

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.. image:: https://img.shields.io/pypi/v/genomicsurveillance.svg

        :target: https://pypi.python.org/pypi/genomicsurveillance

.. image:: https://readthedocs.org/projects/genomicsurveillance/badge/?version=latest

        :target: https://genomicsurveillance.readthedocs.io/en/latest/?badge=latest

        :alt: Documentation Status

Genomic Surveillance is a collection of statistical algorithms to monitor local prevalence of viral lineages.

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Quick install

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Via Pypi

========

To install :code:`genomicsurveillance` via Pypi simply type

.. code-block:: console

    $ pip install genomicsurveillance

into your shell.

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Getting started

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We provide a Google Colab notebook that explains data preparation steps and the usage of the model.

https://colab.research.google.com/drive/1bKEnykFe_gSD_VWk04LWNIsoZiQJ8RcB?usp=sharing

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Credits

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Harald Vöhringer, Matthew Sinnott, Theo Sanderson, Roberto Amato, Inigo Martincorena, Dominic Kwiatkowski, Jeffrey C. Barrett and Moritz Gerstung, on behalf of The COVID-19 Genomics UK (COG-UK)