Delineating inter- and intra-antibody repertoire evolution with AntibodyForests.

IF 5.4

Bioinformatics (Oxford, England) Pub Date : 2025-10-09 DOI:10.1093/bioinformatics/btaf560

Daphne van Ginneken, Valentijn Tromp, Lucas Stalder, Tudor-Stefan Cotet, Sophie Bakker, Anamay Samant, Sai T Reddy, Alexander Yermanos

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Abstract

Motivation: The 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.

Results: Here, 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: This R package is available on CRAN and Github at https://github.com/alexyermanos/AntibodyForests, a vignette is available at https://cran.case.edu/web/packages/AntibodyForests/vignettes/AntibodyForests_vignette.html.

Supplementary information: Supplementary data are available at Bioinformatics online.

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用AntibodyForests描述抗体库之间和内部的进化。

动机：在单细胞技术和人工智能的推动下，免疫库测序的快速发展为以新的规模和分辨率研究B细胞进化创造了前所未有的机会。然而，充分利用这些数据需要专门的软件，能够进行库间和库内分析，以揭示免疫应答过程中B细胞库进化的复杂动态。结果：在这里，我们提出了AntibodyForests软件，用于推断B细胞谱系，量化抗体间和抗体内库进化，并使用蛋白质语言模型和蛋白质结构分析体细胞超突变。可用性：此R包可在CRAN和Github上获得https://github.com/alexyermanos/AntibodyForests，在https://cran.case.edu/web/packages/AntibodyForests/vignettes/AntibodyForests_vignette.html.Supplementary上可获得一个小插图：补充数据可在Bioinformatics在线获得。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Bioinformatics (Oxford, England)

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