Refactor population structure modules with PCA and NJT methods

anopheles-genomic-surveillance / anopheles-genomic-surveillance.github.io

Lecture notes for a course on genomic surveillance of malaria vectors, developed by PAMCA and MalariaGEN

https://anopheles-genomic-surveillance.github.io/

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Refactor population structure modules with PCA and NJT methods #272

Open alimanfoo opened 2 weeks ago

alimanfoo commented 2 weeks ago

The PCA module is hard, and PCAs are just super hard to interpret, lots of people get confused. Genetic distance and neighbour-joining trees are a more intuitive and easier to interpret method.

Propose to:

Create a training module on population structure with neighbour-joining trees, to replace the current PCA module in the entry-level training course.
Migrate the PCA training to an advanced-level module.