An open book on bioinformatics for human genetics: from molecular biology and statistics to biobank-scale genetic association studies, pharmacogenomics, and knowledge graphs.
It is a structured version of years of working notes, organized so that each chapter answers one practical question, with Mermaid diagrams, commands, and checklists.
📖 Read online: https://andrerico.github.io/Bioinformatics/
| Part | Topics |
|---|---|
| I — Foundations | Molecular biology, genetic variation, statistics for describing data, statistical inference |
| II — Data and Infrastructure | Lab and sequencing methods, file formats, computing environment (HPC, cloud), biobanks |
| III — Genetic Association Studies | Genotype QC, relatedness and population structure, GWAS, SAIGE, rare variants, meta-analysis, post-GWAS |
| IV — Applications | Pharmacogenomics, knowledge graphs |
| Appendices | Cheat sheets, templates, reading path, glossary |
Examples that need data use public resources (1000 Genomes, public summary statistics, PharmGKB). No data, results, or infrastructure details from private cohorts appear in the book.
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Install Quarto (version 1.5 or newer).
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From the repository folder:
quarto preview
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The book opens in your browser and reloads every time you save a file.
To build the final version into _book/, run quarto render.
- Conversation, opinions, disagreement: open a Discussion.
- A specific error or suggestion: open an issue with the "Fix or suggestion" template.
- New text or a correction: open a PR. The guide is in CONTRIBUTING.md.
- Book text: CC BY 4.0. Copy and adapt freely, with attribution.
- Code and configuration examples: MIT.
Details in LICENSE.md.
This book is for education and research. It is not medical advice, and nothing in it should be used to make clinical decisions.