clonalstats

Compute clonality statistics and diversity visualizations for TCR/BCR repertoires.

22|4|Updated May 18, 2021

Search Tags:#analysis #tcr #diversity #immune #clonality #bcr #repertoire

Ready to run

npx skills add https://github.com/pwwang/immunopipe --skill clonalstats

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: clonalstats
Source: https://github.com/pwwang/immunopipe/tree/main/skills/clonalstats
Command: npx skills add https://github.com/pwwang/immunopipe --skill clonalstats

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Analyze TCR/BCR repertoires by computing clonality statistics and diversity visualizations, enabling researchers to quantify clonal expansion and compare immune diversity across samples.

Core Features & Use Cases

Quantifies clonal expansion and computes diversity metrics (Shannon, Simpson, Gini).
Generates publication-ready plots to summarize repertoire characteristics across conditions.
Works downstream of ScRepCombiningExpression to analyze integrated TCR+RNA data.

Quick Start

Run ClonalStats after ScRepCombiningExpression to generate clonality statistics and plots for your sample set.

Frequently Asked Questions about clonalstats

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

FAQPage Schema

How do I quantify TCR and BCR clonality and diversity across multiple samples?▼

You can quantify TCR and BCR clonality and diversity across multiple samples by computing clonality statistics and generating diversity visualizations to identify hyperexpanded clones and compare repertoire metrics between conditions.

What diversity metrics are used to measure immune repertoire clonality?▼

Diversity metrics used to measure immune repertoire clonality include the Shannon, Simpson, and Gini indices, which quantify clonal expansion and allow researchers to compare immune diversity across samples and conditions.

How do I generate publication-ready plots for immune repertoire diversity?▼

You generate publication-ready plots for immune repertoire diversity by applying clonality statistics to TCR/BCR repertoires using configurable subset and plotting options that summarize repertoire characteristics across conditions.

Do I need integrated single-cell expression data to analyze TCR clonality?▼

Yes, analyzing TCR clonality requires upstream ScRepCombiningExpression input to integrate TCR and RNA data before computing clonality statistics and diversity visualizations for your samples.

Can I configure chain and clone call settings when computing repertoire diversity?▼

Yes, you can configure clone_call, chain, mutaters, and subset options when computing repertoire diversity, enabling flexible analysis of TCR/BCR repertoires across multiple samples or conditions.