AN
Data & Repro
AnnData
AnnData is a Python package for handling annotated data matrices, storing experimental measurements (X) alongside observation metadata (obs)…
K-Dense-AI/claude-scientific-skillsView
Data & Repro
BI
bio-tcr-bcr-analysis-scirpy-analysis
Maintainer FreedomIntelligence · Last updated April 1, 2026
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.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-tcr-bcr-analysis-scirpy-analysis
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Python: scirpy.io.read_10x_vdj(), scirpy.tl.clonal_expansion(), scirpy.tl.clonotype_network().
- 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().
- adata = sc.read_h5ad('scrnaseq.h5ad').
Source Doc
Excerpt From SKILL.md
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.
import scirpy as ir
import scanpy as sc
## 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')
Use cases
- Use when working with 10x Genomics VDJ data alongside scRNA-seq or when integrating immune receptor information with cell state analysis.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- mixcr-analysis - Process raw VDJ FASTQ
- single-cell/data-io - Load scRNA-seq data
- single-cell/clustering - Cell type annotation
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