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bio-tcr-bcr-analysis-scirpy-analysis

Integrate single-cell TCR/BCR data with gene expression using scirpy.

Updated Mar 30, 2026
Search Tags:#tcr#single-cell#scrna-seq#bcr#repertoire#clonotypes#scirpy
One-click install
npx skills add https://github.com/ya-way/cytoclaw-skills --skill bio-tcr-bcr-analysis-scirpy-analysis
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bio-tcr-bcr-analysis-scirpy-analysis
Source: https://github.com/ya-way/cytoclaw-skills/tree/main/workspace/skills/bio-tcr-bcr-analysis-scirpy-analysis
Command: npx skills add https://github.com/ya-way/cytoclaw-skills --skill bio-tcr-bcr-analysis-scirpy-analysis

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Analyze single-cell TCR and BCR data integrated with gene expression using scirpy. Use when working with 10x Genomics VDJ data alongside scRNA-seq or when integrating immune receptor information with cell state analysis.

Core Features & Use Cases

  • Load VDJ data and attach receptor metadata to AnnData
  • Define clonotypes from CDR3 sequences
  • Assess clonal expansion and repertoire diversity
  • Visualize V gene usage, spectratype, and integrated plots with gene expression
  • Export clonotype summaries for downstream tools

Quick Start

Load your 10x VDJ data into an AnnData object and run clonotype analysis to identify expanded clones.

Frequently Asked Questions about bio-tcr-bcr-analysis-scirpy-analysis

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I integrate single-cell TCR and BCR VDJ data with scRNA-seq gene expression?▼

You can integrate single-cell TCR and BCR VDJ data with gene expression by loading 10x Genomics VDJ data into an AnnData object and attaching receptor metadata to enable joint analysis of clonotypes and cellular states.

How do I define clonotypes from CDR3 sequences in scRNA-seq data?▼

Clonotypes are defined from CDR3 sequences by matching VDJ information to single-cell transcriptomes, allowing you to identify expanded clones and track them across different cell types using scirpy.

Can I visualize V gene usage and spectratype using scirpy with 10x Genomics data?▼

Yes, you can visualize V gene usage and spectratype using scirpy with 10x Genomics VDJ data, generating integrated plots that combine repertoire information with gene expression and cellular states.

What do I need to assess clonal expansion and repertoire diversity in single-cell data?▼

To assess clonal expansion and repertoire diversity, you need scRNA-seq datasets paired with VDJ data in compatible formats, along with scirpy and scanpy to handle data integration, QC, and clonotype definition.

How do I export clonotype summaries for downstream analysis?▼

You can export clonotype summaries after defining clonotypes from CDR3 sequences and assessing clonal expansion, generating output files compatible with downstream tools for further repertoire analysis.

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