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 |
cdr3_length_distribution | CDR3 length frequencies by sample and chain |
amino_acid_summary | Mean CDR3 length and amino-acid property summaries |
positional_entropy | Highest-entropy CDR3 positions with top amino acids |
kmer_usage | Top CDR3 k-mer motifs by sample and chain |
vj_pairing | V/J pairing frequencies |
sample_distance | Pairwise repertoire Jaccard distances |
sample_embedding | Dependency-free sample distance embedding |
barcode_clone_map | Barcode-level clone joins with sample, tissue, timepoint, group, chains, and ambiguity flags |
clone_occupancy | Clone occupancy across barcoded cells, samples, states, and chains |
clonal_bias | Dominant clone associations across state, sample, tissue, timepoint, and group |
clone_alluvial | Clone-flow edges across sample, tissue, timepoint, and cell state |
clone_network | Clonotype-to-cell-state network nodes and edges |
doublet_flags | Ambiguous VDJ barcodes with multiple clonotypes, excess chains, or non-productive contigs |
Diversity metrics
- Shannon entropy
- inverse Simpson index
- clonal evenness
- subsampled rarefaction over observed clonotypes
Advanced sequence summaries
The advanced repertoire slice adds CDR3 sequence summaries used in immunarch/scRepertoire-style review: length distributions, amino-acid property summaries, positional entropy, k-mer usage, V/J pairing, and repertoire distance embeddings. These are descriptive research outputs and do not identify antigen specificity by themselves.
Clone-aware single-cell summaries
For single-cell VDJ tables with barcodes, the pipeline preserves barcode-level joins and reports clone occupancy, clonal bias, clone-flow edges, clone-state networks, and ambiguous VDJ barcode flags. These outputs support clone-aware review without wrapping scRepertoire code.
Reproducibility
Run records include clonotype definition, diversity estimators, advanced repertoire summary names, clone-aware summary names, and minimum clone size.