clonalstats
Generate comprehensive clonality statistics and diversity visualizations for TCR/BCR repertoire analysis. Quantifies clonal expansion, measures diversity metrics (Shannon, Simpson, Gini), and creates publication-ready plots.
npx skills add majiayu000/claude-skill-registry --skill clonalstats-pwwang-immunopipe-2 --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# ClonalStats Process Configuration ## Purpose Generate comprehensive clonality statistics and diversity visualizations for TCR/BCR repertoire analysis. Quantifies clonal expansion, measures diversity metrics (Shannon, Simpson, Gini), and creates publication-ready plots. ## When to Use - To quantify clonal expansion patterns in TCR/BCR data - For diversity analysis comparing multiple samples or conditions - To identify hyperexpanded clones and their distribution - For rarefaction analysis to assess sampling depth - After `ScRepCombiningExpression` to analyze integrated TCR+RNA data ## Configuration Structure ### Process Enablement ```toml [ClonalStats] cache = true ``` ### Input Specification ```toml [ClonalStats.in] screpfile = ["ScRepCombiningExpression"] ``` ### Core Environment Variables ```toml [ClonalStats.envs] # Clone definition: "gene" (VDJC), "aa" (CDR3 amino acid), "nt" (CDR3 nucleotide) clone_call = "aa" # Chain analysis: "both", "TRA", "TRB", "TRG", "IGH", "IGL" chain = "both" # Data transformations (dplyr::mutate syntax) mutaters = {} # Data filtering (dplyr::filter syntax) subset = null # Output device parameters devpars = {width = 800, height = 600, res = 100} # Sav
- Purpose
- When to Use
- Configuration Structure
- Process Enablement
- Input Specification
- Core Environment Variables
- Case-Based Plot Generation
- Diversity Metrics
- Visualization Types
- Configuration Examples
- Minimal Configuration
- Standard Diversity Analysis
- Expanded Clone Analysis
- Rarefaction Analysis
What does the clonalstats skill do?
Generate comprehensive clonality statistics and diversity visualizations for TCR/BCR repertoire analysis. Quantifies clonal expansion, measures diversity metrics (Shannon, Simpson, Gini), and creates publication-ready plots.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill clonalstats-pwwang-immunopipe-2 --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.