README.md

Bioinformatics Portfolio

This repository showcases a comprehensive set of bioinformatics analyses and skills.

Featured: Baseline CD8 exhaustion burden predicts checkpoint-blockade response — end-to-end reanalysis of GSE120575 from raw GEO files. AUROC 0.86 (n=19), replicated across three independent parameterizations.

Projects

1. Variant Analysis Pipeline
2. Sequencing Quality Control
3. Genomic Data Preparation
4. Single-cell RNA-seq Analysis (Seurat)
5. Single-cell RNA Sequencing Analysis (Scanpy)
6. Spatial Transcriptomics Analysis
7. Single-cell ATAC-seq Analysis (Signac/Seurat)
8. Single-cell ATAC-seq Analysis (Scanpy/Episcanpy)
9. ICB Response Biomarker: CD8 Exhaustion Predicts Checkpoint Blockade Response (GSE120575)

Setup

1. Clone this repository
2. Install required Python packages: pip install -r requirements.txt
3. Install required R packages: R -e "install.packages(readLines('r_requirements.txt'), repos='http://cran.rstudio.com/')"
4. Run tests: pytest tests/

Usage

Each analysis can be run independently. See individual documentation in the docs/ directory for details.

Documentation

Detailed documentation for each analysis can be found in the docs directory:

• Variant Analysis
• Sequencing Quality Control
• Genomic Data Preparation
• Single-cell RNA-seq Analysis (Seurat)
• Single-cell RNA-seq Analysis (Scanpy)
• Spatial Transcriptomics Analysis
• Single-cell ATAC-seq Analysis (Signac)
• Single-cell ATAC-seq Analysis (Scanpy)
• ICB Response Biomarker — CD8 Exhaustion

Contact

Syed Nurul Hasan - [nayanchoto1789@gmail.com]