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popgen_course

A course with Jupyter Notebooks for Computational Population Genetics

by Stephan Schiffels

This repository contains several Jupyter Notebooks that I have used in the past for teaching various elements of population-genetic data analyses to students with no initial training in population genetics or Unix-based data analysis. I normally set up these notebooks and the data on a server for people to log into. If you want to try using this material yourself, here are a few steps for settup up your enviroment:

  1. Install Jupyter notebooks with Bash extension. You will also need Eigensoft and ADMIXTOOLS.
  2. Clone this repository in your home directory running git clone https://github.com/stschiff/popgen_course.git
  3. Download the genotype data needed for these exercises from here. In my notebooks, I assume that this data has been downloaded into the directory /data/popgen_course.

Having Jupyter installed, you can now simply open the Notebooks directly from within Jupyter, or you can simply open them directly on github, which will render them nicely as static HTML pages. The chapters are:

  1. Getting Started (Bash)
  2. Getting Started (Python)
  3. Principal Components Analysis (Bash)
  4. Principal Components Analysis (Python)
  5. F Statistics (Python)

In addition to these 5 notebooks, some of the lessons have been kindly translated to R Markdown by @nevrome, in case you would like to see how it's done in R!

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