TCR Clonotype Analysis from Single-Cell RNA-seq

This project analyzes T cell receptor (TCR) sequences from single-cell RNA-seq data using output from the Cell Ranger V(D)J pipeline. It identifies clonally expanded T cells and integrates this information with transcriptomic data for downstream visualization and interpretation.

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📘 Project Overview

This analysis aims to characterize T cell clonal diversity by parsing V(D)J sequencing results and integrating them with scRNA-seq data. The input comes from the all_contig_annotations.csv file generated by the Cell Ranger VDJ pipeline. TCR alpha (TRA), beta (TRB), and paired alpha-beta (TRAB) chains are extracted, saved, and annotated for each cell barcode.

After integration with Seurat RNA data, cells are categorized as:

• no_TCR: cells with no detected TCR
• unique_TCR: cells with a private (non-shared) clonotype
• clonal_TCR: cells that share the same clonotype (expanded clones)

UMAP plots are used to visualize these clonotype categories across the transcriptomic landscape.

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📊 Analysis Tasks

Task 1: Parsing and Saving TCR Chain Information

• Read all_contig_annotations.csv from Cell Ranger output
• Filter and separate entries into:
  • TRA (alpha)
  • TRB (beta)
  • TRAB (paired chains)
• Save cleaned clonotype assignments for downstream integration

Task 2: Integration with Seurat and Visualization

• Load Seurat RNA-based object
• Add TCR clonotype information to cell metadata
• Categorize cells into: no_TCR, unique_TCR, and clonal_TCR
• Visualize clonotype categories on UMAP (e.g., group.by = "clonotype_status")

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💡 Notes

• Raw data is not publicly available due to client ownership and confidentiality.
• Some example outputs plots are organized by task in the output/ folder.
• This project is designed for both reproducibility and clarity.

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📬 Contact

Author: Nasim Rahmatpour Email: nasimrahmatpour1@gmail.com GitHub: (https://github.com/nasimbio)