influenza-global-reassortment

Jupyter notebooks and data - reproducible analysis from reassortment paper.

To re-run these analyses, run the code in the following notebooks:

For a tutorial on how to run Jupyter notebooks, see the Jupyter project website.

Software requirements:

To visualize lineage traces of the 2009 H1N1 or 2013 H7N9 viruses, do the following:

Clone the repository to disk.
Navigate to the directory supp_data/viz
Start a web server in the directory. One option is to use python -m http.server 8000. This starts a local web server in the directory with port 8000.
In your browser, type: localhost:8000/h1n1.html. Replace the port number accordingly; to visualize H7N9, use h7n9.html instead.

Name		Name	Last commit message	Last commit date
Latest commit History 111 Commits
.ipynb_checkpoints		.ipynb_checkpoints
figures		figures
md_final_graphs		md_final_graphs
supp_data		supp_data
.gitignore		.gitignore
20150902_all_ird Final Graph.pkl		20150902_all_ird Final Graph.pkl
20150902_all_ird Full Complement Graph.pkl		20150902_all_ird Full Complement Graph.pkl
Basic Graph Statistics.ipynb		Basic Graph Statistics.ipynb
Data Checks (Prototype Code).ipynb		Data Checks (Prototype Code).ipynb
Data Preprocessing - Host COI distance.ipynb		Data Preprocessing - Host COI distance.ipynb
LICENSE		LICENSE
Make Figure - Highly Reassorting Subtypes.ipynb		Make Figure - Highly Reassorting Subtypes.ipynb
Make Figure - Known Transmission Patterns.ipynb		Make Figure - Known Transmission Patterns.ipynb
Make Figure - PWI Histogram.ipynb		Make Figure - PWI Histogram.ipynb
Make Figure - Proportion Reassortant.ipynb		Make Figure - Proportion Reassortant.ipynb
Make Figures - Median Downsampled Set.ipynb		Make Figures - Median Downsampled Set.ipynb
Make Supplementary Data - Edge List and Node List.ipynb		Make Supplementary Data - Edge List and Node List.ipynb
Quick Data Checks.ipynb		Quick Data Checks.ipynb
README.md		README.md
Revisions - How "conservative" is the cutoff of 10 percent?.ipynb		Revisions - How "conservative" is the cutoff of 10 percent?.ipynb
Revisions - Lineage Traces.ipynb		Revisions - Lineage Traces.ipynb
Revisions - Mallards and Gulls.ipynb		Revisions - Mallards and Gulls.ipynb
custom_funcs.py		custom_funcs.py
figures.py		figures.py

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