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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