Compute clonality statistics and diversity visualizations for TCR/BCR repertoires.
npx skills add https://github.com/pwwang/immunopipe --skill clonalstats
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
Analyze TCR/BCR repertoires by computing clonality statistics and diversity visualizations, enabling researchers to quantify clonal expansion and compare immune diversity across samples.
Run ClonalStats after ScRepCombiningExpression to generate clonality statistics and plots for your sample set.
High-intent search queries and answers about installing and using this skill.
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.
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.
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.
Yes, analyzing TCR clonality requires upstream ScRepCombiningExpression input to integrate TCR and RNA data before computing clonality statistics and diversity visualizations for your samples.
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.
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