A set of lectures on Genome Wide Association Studies (GWAS) with Limix, Python and Jupyter Notebooks. The notebooks are heavily based on the original limix tutorial notebooks but adapted to work with the latest stable Limix 1.x release.
To open these notebooks in Jupyter, download the files to a directory on your computer and from that directory run (for installation of the necessary software packages see Lecture-0 Setup of Python Environment):
$ jupyter notebook
Use the following links:
- Lecture 0 - Setup of Python Environment
- Lecture 1 - Introduction to Jupyter Notebooks
- Lecture 2 - Introduction to Python-Programming
- Lecture 3 - Introduction to Numpy
- Lecture 4 - Matplotlib
- Lecture 5 - HDF5 h5py PyTables
- Lecture 6 - Linear Regression
- Lecture 7 - Linear Mixed Model
- Lecture 8 - Multi Trait Linear Mixed Model
- Lecture 9 - Estimating (SNP) narrow-sense heritability
- Lecture 10 - Estimating (SNP) broade-sense heritability
This work is licensed under a Creative Commons Attribution 3.0 Unported License.