geovar is a python package to visualize joint allele frequency spectrum data.
You can find a webpage introducing the software (with installation instructions, a tutorial, and API documentation) at the following url: https://aabiddanda.github.io/geovar/
The geovar software was developed by Arjun Biddanda, with contributions from Daniel P. Rice and John Novembre.
We highly recommend installing the package via pip.
pip install git+https://github.com/aabiddanda/geovar
or to install the package locally:
git clone https://github.com/aabiddanda/geovar
cd geovar
pip install .
If you are interested in a working tutorial of the geovar library, please either look at the static version under the "Tutorial" section of our documetation here.
For a more engaging experience, please click the Launch Binder link at the top of this README, which offers an interactive tutorial in a jupyter notebook.
If you use geovar in your publication, we kindly ask that you cite the following manuscript:
Arjun Biddanda, Daniel P Rice, John Novembre.
*A variant-centric perspective on geographic patterns of human allele frequency variation.* (eLife) 2020.
You can also find an open-access version of the paper here.
If you find a bug in the code - please submit an issue. If you have feature requests or questions please post an issue or email aabiddanda[at]gmail.com.