bio-tcr-bcr-analysis-scirpy-analysis

name	bio-tcr-bcr-analysis-scirpy-analysis
description	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.
tool_type	python
primary_tool	scirpy

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.