Bioninformatics & Biostatistics Training

Material from courses, training and research activities.

• notes
• theoretical insights
• worked out notebooks with exercises (R, Python)

First project

1. super-quick recap of linear mixed models
2. application to genetics and breeding: from BLUP to GBLUP
3. an alternative parameterization: the SNP-BLUP
4. how to do cross-validation with SNP-BLUP
5. how to do cross-validation with GBLUP

Course "Introduction to animal breeding" - University of Pisa (1st year BSc)

1. basic statistics
2. matrix algebra recap (super-quick)
3. general introduction to animal breeding
4. heritability estimation
5. pedigree and kinship matrices
6. enter genomics: genomic relationship matrices
7. runs of homozygosity (ROH) and genomic inbreeding
8. mixed models: BLUP and GBLUP
9. multiple trait models and genetic correlations
10. selection index theory
11. brief introduction to deep learning
12. models for image recognition: computer vision for veterinary diagnosis (and for genomic selection)

Resources

• R : The Comprehensive R Archive Network (CRAN)
• Python: The Python Tutorial