domains / families / science / immcantation-analysis

immcantation-analysis

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Reconstructs B-cell clonal families, quantifies somatic hypermutation and selection, and builds antibody lineage trees with the Immcantation R suite (alakazam, shazam, scoper, dowser, tigger) on AIRR-format BCR data. Use when deriving the clonal-clustering threshold from the distToNearest bimodal valley (never a hardcoded 0.15); choosing hierarchicalClones vs spectralClones (vj vs novj) for SHM-diverged repertoires; personalizing the germline with TIGGER before mutation counting; reconstructing D-masked germlines with createGermlines; measuring R/S mutation frequency by CDR and FWR region; testing antigen-driven selection with BASELINe; comparing Hill-number diversity at equal sampling depth; and inferring IgPhyML lineage trees for affinity maturation, class-switch, and ancestral-antibody analysis.

When to use

• Reconstructing B-cell clonal families
• Quantifying somatic hypermutation
• Building antibody lineage trees
• Deriving clonal-clustering threshold from distToNearest
• Personalizing germline with TIGGER
• Reconstructing D-masked germlines
• Measuring R/S mutation frequency
• Testing antigen-driven selection

When not to use

• Hardcoding clonal threshold to 0.15
• Using exact-CDR3 matching for BCR
• Using amino-acid junction distance

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