Cluster TCR/BCR clones by CDR3 sequences using GIANA or ClusTCR.
npx skills add https://github.com/pwwang/immunopipe --skill cdr3clustering
Please help me install this Agent Skill. Skill: cdr3clustering Source: https://github.com/pwwang/immunopipe/tree/main/skills/cdr3clustering Command: npx skills add https://github.com/pwwang/immunopipe --skill cdr3clustering
Clustering of TCR/BCR clones by CDR3 sequences to reveal related clonotypes and public motifs, enabling downstream clonotype analysis.
Run the CDR3Clustering process on your TCR/BCR data to generate the CDR3_Cluster metadata.
High-intent search queries and answers about installing and using this skill.
Cluster TCR/BCR clones by CDR3 sequences using GIANA or ClusTCR to group related clonotypes and generate a CDR3_Cluster metadata field for downstream analysis. The process supports per-sample or cross-sample clustering.
Cross-sample CDR3 clustering identifies public clonotypes by revealing convergent recombination and shared motifs across your dataset. You can configure the clustering threshold to suit your analysis goals.
CDR3 clustering supports T-cell receptor chains (TRA/TRB) and B-cell receptor chains (IGH/IGL/IGK). You can flexibly select the specific chains to cluster based on your dataset and analysis goals.
Clustering CDR3 sequences requires TCR/BCR data outputs from ScRepCombiningExpression. The process validates required dependencies and environment settings to ensure your data is properly formatted for clustering.
Choose GIANA or ClusTCR based on your dataset size and analysis goals. Both use Faiss-based methods to cluster CDR3 sequences, but you can select the tool and configure threshold options to suit your specific clonotype analysis needs.
Faiss provides efficient similarity search for clustering large sets of CDR3 sequences. GIANA and ClusTCR rely on Faiss to rapidly group related TCR/BCR clonotypes, enabling the identification of public motifs across samples.
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