bio-tcr-bcr-analysis-scirpy-analysis
Analyze single-cell TCR and BCR data integrated with gene expression using scirpy. Use when working with 10x Genomics VDJ data alongside scRNA-seq or when integrating immune receptor information with cell state analysis.
npx skills add majiayu000/claude-skill-registry --skill scirpy-analysis --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.
# scirpy Analysis ## Load VDJ Data ```python import scirpy as ir import scanpy as sc # Load 10x VDJ data adata = sc.read_h5ad('scrnaseq.h5ad') # Add VDJ annotations from 10x filtered_contig_annotations.csv ir.io.read_10x_vdj(adata, 'filtered_contig_annotations.csv') # Or load from AIRR format ir.io.read_airr(adata, 'airr_rearrangement.tsv') ``` ## Quality Control ```python # QC for receptor chains ir.tl.chain_qc(adata) # QC categories: # - multichain: More than 2 chains (potential doublet) # - orphan: Only one chain detected # - extra: Extra chains beyond expected pair # - ambiguous: Ambiguous chain pairing # Plot QC ir.pl.group_abundance(adata, groupby='chain_pairing', target_col='receptor_subtype') ``` ## Define Clonotypes ```python # Define clonotypes by CDR3 sequence identity ir.pp.ir_dist( adata, metric='identity', sequence='aa', cutoff=0 ) ir.tl.define_clonotypes(adata, receptor_arms='all', dual_ir='primary_only') # Check clonotype distribution print(f"Unique clonotypes: {adata.obs['clone_id'].nunique()}") ``` ## Clonal Expansion ```python # Identify expanded clonotypes ir.tl.clonal_expansion(adata) # Categories: 1 (singleton), 2, 3-10, >10 # Plot expansion by cell type ir.pl
- Load VDJ Data
- Quality Control
- Define Clonotypes
- Clonal Expansion
- Repertoire Diversity
- Compare Groups
- V(D)J Gene Usage
- Integration with Gene Expression
- Export for Downstream Analysis
- Related Skills
What does the bio-tcr-bcr-analysis-scirpy-analysis skill do?
Analyze single-cell TCR and BCR data integrated with gene expression using scirpy. Use when working with 10x Genomics VDJ data alongside scRNA-seq or when integrating immune receptor information with cell state analysis.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill scirpy-analysis --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.