cdr3clustering
Cluster TCR/BCR clones by CDR3 sequences using GIANA or ClusTCR (both Faiss-based). Adds `CDR3_Cluster` column to metadata for clonotype analysis.
npx skills add majiayu000/claude-skill-registry --skill cdr3clustering --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.
# CDR3Clustering Process Configuration ## Purpose Cluster TCR/BCR clones by CDR3 sequences using GIANA or ClusTCR (both Faiss-based). Adds `CDR3_Cluster` column to metadata for clonotype analysis. ## When to Use - To identify groups of similar TCR/BCR clonotypes - For analyzing TCR sequence convergence - After ScRepCombiningExpression when TCR/BCR integrated with RNA - For investigating public clonotypes across samples - Before TESSA analysis for epitope specificity **Important**: Only runs when VDJ input present (TCRData/BCRData columns in SampleInfo). ## Configuration Structure ### Process Enablement ```toml [CDR3Clustering] cache = true ``` ### Input Specification ```toml [CDR3Clustering.in] screpfile = "path/to/combined_object.qs" ``` ### Environment Variables ```toml [CDR3Clustering.envs] type = "auto" # TCR, BCR, or auto tool = "GIANA" # GIANA or ClusTCR python = "python" # Path to python within_sample = true # Cluster per sample args = {} # Tool-specific arguments chain = "both" # TRA, TRB, IGH, IGL, IGK, both, heavy, light ``` #### GIANA Arguments (via `args`) ```toml [CDR3Clustering.envs.args] method = "hierarchical" # hierarchical, kmeans dist = "hamming" # hamming, leven
- Purpose
- When to Use
- Configuration Structure
- Process Enablement
- Input Specification
- Environment Variables
- Configuration Examples
- Minimal Configuration
- GIANA with Custom Distance Threshold
- ClusTCR Two-Step (Large Datasets)
- ClusTCR MCL (Small Datasets)
- TRB Chain Only
- Cross-Sample Clustering
- Common Patterns
What does the cdr3clustering skill do?
Cluster TCR/BCR clones by CDR3 sequences using GIANA or ClusTCR (both Faiss-based). Adds `CDR3_Cluster` column to metadata for clonotype analysis.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill cdr3clustering --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.