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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-tcr-bcr-analysis-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.
## Version Compatibility Reference examples tested with: MiXCR 4.6+, VDJtools 1.2.1+, scanpy 1.10+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # scirpy Analysis **"Analyze single-cell TCR/BCR with gene expression"** → Integrate immune receptor clonotype data with scRNA-seq gene expression for joint analysis of clonal expansion and cell state. - Python: `scirpy.io.read_10x_vdj()`, `scirpy.tl.clonal_expansion()`, `scirpy.tl.clonotype_network()` ## Load VDJ Data **Goal:** Import single-cell VDJ annotations and integrate them with an existing scRNA-seq AnnData object. **Approach:** Read 10x filtered_contig_annotations or AIRR-format files and attach receptor metadata to the AnnData obs. ```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')
- Version Compatibility
- 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-tcr-bcr-analysis-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 FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 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.