TCR/BCR repertoire
The repertoire_analysis pipeline is the canonical Immunology engine for TCR/BCR repertoire methods. Oncology calls this shared engine for repertoire summaries.
Inputs
Supported tabular inputs include:
- 10x Immune Profiling contig annotations
- AIRR-style fields
- bulk TCR/BCR CSV or TSV tables
- inline rows for small tests
Outputs
| Output | Description |
|---|---|
sample_summaries | Clonotype counts, templates, expansion counts, diversity, rarefaction summaries |
v_gene_usage | V gene counts and frequencies |
j_gene_usage | J gene counts and frequencies |
top_clonotypes | Top clones and expansion classes |
clone_state_links | Clonotype-to-cell-state summaries |
overlap | Cross-sample Jaccard and shared clonotype fractions |
public_private | Public/private clone classification |
Diversity metrics
- Shannon entropy
- inverse Simpson index
- clonal evenness
Reproducibility
Run records include clonotype definition, diversity estimators, and minimum clone size.