scRNA-seq Analysis Assignment

Overview

This repository contains three single-cell RNA-seq tutorials completed as part of a bioinformatics assignment.

Tutorials

1. Pre-processing of 10X Single-Cell RNA Datasets

• Tool: Galaxy Platform (STARsolo + DropletUtils)
• Data: 1k PBMCs from healthy donor
• Results: 254 high quality cells detected
• 🔗 Repository

2. Basic scRNA-seq Tutorial with Scanpy

• Tool: Python/Scanpy (Google Colab)
• Data: Bone marrow mononuclear cells (NeurIPS 2021)
• Results: 17,041 cells, 18 clusters identified
• 🔗 Repository

3. AnnData Tutorial

• Tool: Python/AnnData (Google Colab)
• Data: Synthetic + PBMC68k dataset
• Results: AnnData object creation and manipulation
• 🔗 Repository

Tools Used

Tool	Purpose
Galaxy	Cloud bioinformatics platform
STARsolo	RNA mapping & quantification
DropletUtils	Cell filtering
Scanpy	scRNA-seq analysis
AnnData	Data structure
Python	Programming

Reference

• Galaxy Tutorial
• Scanpy Tutorial
• AnnData Docs