Bioinformatics Analysis Templates

This repository contains modular R/bash pipelines and example datasets for common bioinformatics workflows. It includes end-to-end analysis scripts and results for:

• 🧬 Bulk RNA-Seq differential expression analysis (DESeq2)
• 🌡 Heatmap generation
• 🌋 Volcano plot visualization
• 🧬 VCF filtering for WES-derived variant files
• 🧪 Weighted Gene Co-expression Network Analysis (WGCNA)
• 🔁 Raw RNA-Seq data preprocessing from FASTQ to Count Matrix

⚠️ All data and results are included for demonstration purposes only and contain no real patient identifiers or confidential content.

📁 Folder Structure

Bioinformatics-Templates/ ├── README.md ├── CITATION.cff ├── LICENSE ├── demo_analysis.Rmd ├── deseq2/ # DESeq2 pipeline + example data ├── heatmap/ # Heatmap template + matrix ├── volcano/ # Volcano plot script + matrix ├── vcf_filtering/ # VCF filtering script + demo data ├── Raw_FASTQ_to_CountMatrix/ # Raw FASTQ → Count Matrix Bash pipeline │ └── scripts/ ├── GSE148355_WGCNA/ # WGCNA analysis example on GEO dataset

📜 Scripts Overview

| Script Name | Description | |----------------------------|-----------------------------------------------------------------------------| | DESeq2_pipeline.R | Normalize RNA-Seq counts and identify DEGs | | Heatmap_Template.R | Generate clustered heatmap from expression matrix | | volcano_plot.R | Create volcano plot of DEGs from DESeq2 results | | VCF_Filtering.R | Apply filters to VCF files based on quality/depth/etc. | | pipeline.sh | Bash pipeline from fastq-dump to htseq-count | | WGCNA_analysis.R | Full WGCNA pipeline using GSE148355 dataset |

📂 Sample Data

| File | Description | |----------------------------|-----------------------------------------------------------| | example_counts.txt | Simulated raw count matrix | | example_metadata.csv | Sample metadata with group labels | | expression_matrix.csv | Expression matrix for heatmap/volcano | | myvcf.vcf | Demo VCF file for variant filtering | | vcf_filtered.csv | Filtered VCF output | | GSE148355_raw_counts.csv | Real RNA-Seq counts from GEO | | traits.csv | Sample traits (e.g. group, gender, age) |

🚀 How to Use

1. Clone the repository: bash git clone https://github.com/somayehsarirchi/Bioinformatics-Templates.git cd Bioinformatics-Templates

2. Navigate to the relevant analysis folder (e.g., deseq2/, GSE148355_WGCNA/)

3. Run the script in R, RStudio, or terminal: r source("DESeq2_pipeline.R")

4. Render the demo notebook (optional): Open demo_analysis.Rmd in RStudio and click Knit to generate the report.

⚙️ Requirements

• R version ≥ 4.2
• Tools: sratoolkit, HISAT2, HTSeq
• Required R packages: DESeq2, WGCNA, pheatmap, ggplot2, readr, Hmisc, enrichR, etc.
• Bash and Java (for FASTQ processing)

📜 License

This project is licensed under the MIT License.

📦 Citation

If you use this repository or its scripts, please cite it as:

Somayeh Sarirchi (2025). Bioinformatics Analysis Templates: RNA-seq, VCF filtering, and Visualization Pipelines. GitHub repository: https://github.com/somayehsarirchi/Bioinformatics-Templates
DOI: 10.5281/zenodo.16493302

👩‍🔬 Author

Somayeh Sarirchi
Bioinformatics Scientist
📧 s.sarirchi@gmail.com
🔗 GitHub Profile