biomedical-knowledge-mining-book

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biomedical-knowledge-mining-book

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:book: Biomedical knowledge mining using GOSemSim and clusterProfiler

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# Biomedical Knowledge Mining using GOSemSim and clusterProfiler

This repository contains the source code and content for the book **"Biomedical Knowledge Mining using GOSemSim and clusterProfiler"** authored by Guangchuang Yu.

## About the Book

This book provides a comprehensive guide to biomedical knowledge mining, focusing on functional enrichment analysis and semantic similarity using popular R packages such as `clusterProfiler`, `GOSemSim`, `DOSE`, `enrichit`, and `meshes`.

Key topics covered include:
- **Semantic Similarity**: Computations across GO, DO, and MeSH.
- **Enrichment Algorithms**: In-depth explanations of Over-Representation Analysis (ORA), Gene Set Enrichment Analysis (GSEA), Network-based Set Enrichment Analysis (NSEA), and Weighted Enrichment.
- **Database Integrations**: Functional analysis across diverse databases including Gene Ontology (GO), KEGG, Reactome, Disease Ontology, and more.
- **Visualization & Interpretation**: Powerful plotting methods and Bayesian term selection to interpret complex biological data.

## Read Online

The compiled and up-to-date version of this book is available online at:  
👉 **[https://yulab-smu.top/biomedical-knowledge-mining-book/](https://yulab-smu.top/biomedical-knowledge-mining-book/)**

## Contributing

Contributions, bug reports, and suggestions are welcome. Please feel free to open an issue or submit a pull request on our [GitHub repository](https://github.com/YuLab-SMU/biomedical-knowledge-mining-book/).

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