Repertoire diversity
Use this workflow to study TCR/BCR clonotypes, expansion, diversity, sequence features, and clone-state relationships. It supports both bulk repertoire review and single-cell VDJ analysis where barcode-level clone assignments need to be connected to immune phenotype, tissue, timepoint, or disease context.
Research question
Which clones are expanded, shared, phenotype-linked, or ambiguous, and how do repertoire diversity and CDR3 sequence features vary across samples, tissues, timepoints, or disease groups?
Use case
Use this when the biological question depends on clonal expansion, public/private clones, V/J usage, sequence properties, or single-cell clone occupancy. The workflow is especially useful for vaccine, infection, autoimmunity, cell therapy, and immuno-oncology studies where receptor expansion must be interpreted alongside immune cell state.
Suggested path
- Register a
vdjdataset. - Run
repertoire_analysis. - Review diversity, expansion, V/J usage, V/J pairing, CDR3 summaries, k-mers, entropy, sample distances, clone occupancy, clonal bias, barcode clone maps, and overlap.
- Use disease workflows or interpretation to contextualize clone-state patterns.
Outputs to cite
- Shannon entropy
- inverse Simpson index
- clonal evenness
- top clonotypes
- shared clonotype fractions
- CDR3 length and amino-acid property summaries
- positional entropy and k-mer usage
- V/J pairing frequencies
- sample distance embedding
- barcode-to-clone map
- clone occupancy and clonal bias
- clone-flow and clone-state network edges
- VDJ ambiguity flags