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blab / cartography

Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2
https://doi.org/10.1101/2024.02.07.579374
MIT License
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Add workflow to test effects of genetic bias #69

Closed huddlej closed 8 months ago

huddlej commented 10 months ago

Adds workflow for late seasonal flu data to test the effects of genetic bias on embedding methods. Runs the same general steps as the main late flu workflow (alignment, tree, embeddings, clusters), calculates the accuracy of the embeddings vs. Nextstrain clades for comparison with the late flu data, and plots the relationship between Euclidean and genetic distances in the biased sample.

huddlej commented 8 months ago

Closing this in favor of https://github.com/blab/cartography/commit/3982b9a9a8a948b72d2424cd86b3c088a40a703d