This repository provides the source code, scripts, and usage instructions that serve as supplementary materials for the book Bioinformatics of Autoimmune Diseases. It is designed to support reproducibility and hands-on learning by offering practical examples, data analysis pipelines, and tools discussed throughout the chapters.

The repository is organized into directories corresponding to chapters in the book:

• ch4/ – Bioinformatics Databases
• ch5/ – RNA Sequencing (RNA-Seq and Small RNA-Seq)
• ch6/ – Variant Analysis
• ch7/ – ChIP-Seq for DNA-Protein Interaction
• ch8/ – ATAC-Seq for Autoimmune Diseases
• ch9/ – Amplicon-Based and Shotgun-Based Metagenomics Data Analysis

Each chapter contains relevant code, scripts, and setup instructions.

Before running the code, please ensure the following:

• A Linux-based system is strongly recommended, preferably a high-performance computing (HPC) environment.
• Sufficient memory and storage capacity to process large datasets.
• All required software and packages must be installed as noted in the comments within each script.
• It is recommended to create a separate Anaconda environment for each chapter to manage dependencies cleanly.

• Download the example raw data using the provided scripts located in the data/raw/ directory.
• Reference genomes, annotation files, and databases should be downloaded and configured as described in the corresponding book chapters.
• Ensure you update file paths in the scripts to reflect your local setup.

Check this repository periodically for updates, bug fixes, and additional resources.

If you use this repository or any of the materials in your work, please cite the book as follows:

Ismail, Hamid D. Bioinformatics of Autoimmune Diseases. Under publishing.

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