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bioRxiv · 10.1101/2025.03.11.642619

Delineating inter- and intra-antibody repertoire evolution with AntibodyForests

van Ginneken, D.·Tromp, V.·Stalder, L.·Cotet, T.-S.·Bakker, S.·Samant, A.·Reddy, S. T.·Yermanos, A.
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Abstract

MotivationThe rapid advancements in immune repertoire sequencing, powered by single-cell technologies and artificial intelligence, have created unprecedented opportunities to study B cell evolution at a novel scale and resolution. However, fully leveraging these data requires specialized software capable of performing inter- and intra-repertoire analyses to unravel the complex dynamics of B cell repertoire evolution during immune responses. ResultsHere, we present AntibodyForests, software to infer B cell lineages, quantify inter- and intra-antibody repertoire evolution, and analyze somatic hypermutation using protein language models and protein structure. Availability and implementationThis R package is available on CRAN (1) and Github at https://github.com/alexyermanos/AntibodyForests, a vignette is available at https://cran.case.edu/web/packages/AntibodyForests/vignettes/AntibodyForests_vignette.html

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van Ginneken, D., Tromp, V., Stalder, L., Cotet, T.-S., Bakker, S., Samant, A., Reddy, S. T., Yermanos, A.. 2025-03-12. Delineating inter- and intra-antibody repertoire evolution with AntibodyForests. https://doi.org/10.1101/2025.03.11.642619

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