Single-cell Immune & TCR Repertoire Analysis

Overview

This repository contains computational workflows for single-cell RNA-seq and TCR repertoire analysis in paediatric immune datasets.

The project investigates:

• Immune ageing dynamics
• T-cell compositional changes
• Differential abundance patterns
• TCR clonotype expansion
• Repertoire diversity and transcriptomic integration

Analyses were performed in Linux-based HPC environments using reproducible Python and R workflows.

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Analysis Components

Single-cell RNA-seq Analysis

• Quality control and preprocessing
• Batch correction and integration using scVI
• Dimensionality reduction and clustering
• UMAP visualisation
• Cell type annotation using canonical marker expression

Differential Abundance Analysis

• Milo neighbourhood-based differential abundance testing
• scCODA compositional modelling
• Age- and sex-associated abundance analysis

TCR Repertoire Analysis

• TCR integration using Dandelion
• Clonotype expansion analysis
• Clone size categorisation
• Repertoire diversity analysis
• TCR-transcriptome integration

Statistical Visualisation

• UMAP visualisation
• Differential abundance plots
• Clonotype distribution analysis
• Composition and repertoire visualisation

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Tools & Packages

Python

• Scanpy
• scVI-tools
• Dandelion
• Milo
• PertPy
• pandas
• NumPy
• matplotlib
• seaborn

R

• MiloR
• tidyverse
• ggplot2

Infrastructure

• Linux
• HPC environments (Bunya)
• bash
• conda
• Jupyter Notebook

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Repository Structure

notebooks/      Analysis notebooks
scripts/        Reusable workflow scripts
Results/        Analysis outputs and figures
dandelion/      TCR repertoire workflows
workflow/       Pipeline diagrams and workflow notes
environment/    Package and environment specifications

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Workflow Overview

Raw scRNA-seq + VDJ data
                ↓
Quality control and filtering
                ↓
Batch correction / integration (scVI)
                ↓
Dimensionality reduction and clustering
                ↓
Cell type annotation
                ↓
Differential abundance analysis
        ↙                     ↘
     Milo                  scCODA
                ↓
TCR integration (Dandelion)
                ↓
Clonotype expansion analysis
                ↓
Clone size categorisation
                ↓
Repertoire diversity analysis
                ↓
Statistical visualisation and interpretation

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Skills Demonstrated

• Single-cell RNA-seq analysis
• Cell type annotation
• Differential abundance modelling
• TCR clonotype analysis
• Immune repertoire analysis
• Statistical visualisation
• HPC workflow management
• Reproducible computational biology pipelines

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Notes

Raw sequencing datasets are not included in this repository.

This repository focuses on reproducible downstream computational workflows and analyses.