bio-tcr-bcr-analysis-immcantation-analysis

To analyze BCR repertoires for somatic hypermutation and clonal evolution, you can use the Immcantation framework to load AIRR-formatted data, cluster clonal lineages, quantify mutations, and build lineage trees.

You can build lineage trees from AIRR-formatted BCR data by loading your sequences into the Immcantation workflow, which integrates dowser to reconstruct and visualize ancestral relationships for multi-sequence clones.

Yes, you can infer germline alleles and test for selection in BCR sequences using R by integrating the tigger and shazam packages within the Immcantation framework to analyze affinity maturation dynamics.

The Immcantation framework supports cohort-level BCR clonality analysis by processing AIRR-formatted data across multiple individuals, allowing you to cluster sequences and generate publishable reports for the entire cohort.

The best way to integrate alakazam and shazam for antibody dynamics analysis is through an end-to-end Immcantation workflow that handles V(D)J annotation, clonality clustering, and selection testing in a single run.