Gut Microbiome Analysis for CRC Detection

This repository contains the source code for the book "Gut Microbiome Analysis for CRC Detection: From Raw Sequences to Machine Learning Models," created using Quarto. The book is available online at https://pankajchejara23.github.io/bioinformatics_book/.

Project Structure

├── _quarto.yml          # Quarto project configuration
├── index.qmd            # Homepage for the book
├── chapters/            # Directory containing individual chapter files
├── docs/                # Rendered HTML files
├── images/              # Figures and images used in the book
├── data/                # Datasets used in examples
└── README.md            # This file

Key Files and Directories

• _quarto.yml: Defines the global settings for the book, including the title, author, and output format.
• index.qmd: The main landing page for the book.
• chapters/: Contains the .qmd and .ipynb files for each chapter.
• docs/: Contains rendered html files.
• images/: Stores all images and figures used throughout the book.
• data/: Includes datasets required for code examples and analysis.

Prerequisites

To build this book locally, you'll need:

1. Quarto: Install from Quarto's official website.
2. R or Python: Depending on the code examples in the book, install the necessary runtime.
3. Packages: Install any additional dependencies required for the code snippets.

How to Build the Book

1. Clone the repository:

   git clone https://github.com/pankajchejara23/bioinformatics_book.git
   cd bioinformatics_book

2. Render the book locally:

   quarto render

3. Open the generated HTML files located in the docs/ directory in your browser.

License

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. © 2025 Pankaj Chejara

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