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bio-tcr-bcr-analysis-scirpy-analysis

维护者 FreedomIntelligence · 最近更新 2026年4月1日

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.

OpenClawNanoClaw分析处理复现实验bio-tcr-bcr-analysis-scirpy-analysis🧬 bioinformatics (gptomics bio-* suite)bioinformatics — immunoinformatics & flow cytometryanalyze

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-tcr-bcr-analysis-scirpy-analysis

维护者
FreedomIntelligence
许可
MIT
最近更新
2026年4月1日

技能摘要

来自 SKILL.md 的关键信息

2 min

核心说明

  • Python：scirpy.io.read_10x_vdj()，scirpy.tl.clonal_expansion()，scirpy.tl.clonotype_network()。
  • 分析 single-cell TCR/BCR ，支持 gene expression" → Integrate immune receptor clonotype data ，支持 scRNA-seq gene expression ，用于 joint analysis of clonal expansion 、 cell state. Python：scirpy.io.read_10x_vdj()，scirpy.tl.clonal_expansion()，scirpy.tl.clonotype_network()。
  • adata = sc.read_h5ad('scrnaseq.h5ad')。

原始文档

SKILL.md 摘录

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')

适用场景

  • 适合在working ，支持 10x Genomics VDJ data alongside scRNA-seq 或 when integrating immune receptor information ，支持 cell state analysis时使用。

不适用场景

  • Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。

上游相关技能

  • mixcr-analysis - Process raw VDJ FASTQ
  • single-cell/data-io - Load scRNA-seq data
  • single-cell/clustering - Cell type annotation

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