README.md
In AntibodyForests: Delineating Inter- And Intra-Antibody Repertoire Evolution

Delineating inter- and intra-antibody repertoire evolution with AntibodyForests

The generated wealth of immune repertoire sequencing data requires software to investigate and quantify inter- and intra-antibody repertoire evolution to uncover how B cells evolve during immune responses. Here, we present AntibodyForests, a software to investigate and quantify inter- and intra-antibody repertoire evolution.

This R package is currently composed of a pipeline to reconstruct lineage trees from 10x single-cell V(D)J sequencing data preprocessed with the Platypus package and compare trees within and across repertoires. Furthermore, it has modalities to integrate bulk RNA sequencing data, features of protein 3D structure, and evolutionary likelihoods generated with protein language models.