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/

Contributing

Contributions, bug reports, and suggestions are welcome. Please feel free to open an issue or submit a pull request on our GitHub repository.