Delineating Inter- And Intra-Antibody Repertoire Evolution [R package AntibodyForests version 1.1.0]

AntibodyForests: Delineating Inter- And Intra-Antibody Repertoire Evolution

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.

Version: 1.1.0

Depends: R (≥ 4.0.0)

Imports: ape, Biostrings, dplyr, graphics, grDevices, gtools, igraph, magrittr, parallel, pwalign, rlang, scales, seqinr, stats, stringdist, stringr, tidyr, utils, viridis

Suggests: alakazam, base64enc, bio3d, combinat, devtools, DT, fpc, ggplot2, ggrepel, ggsignif, htmltools, knitr, msa, phangorn, pheatmap, philentropy, Peptides, Rcompadre, rmarkdown, RPANDA, swipeR

Published: 2025年07月17日

DOI: 10.32614/CRAN.package.AntibodyForests

Author: Daphne van Ginneken [aut, cre], Alexander Yermanos [aut], Valentijn Tromp [aut], Tudor-Stefan Cotet [ctb]

Maintainer: Daphne van Ginneken <daphne.v.ginneken at gmail.com>

License: GPL-2

NeedsCompilation: no

Materials: README

CRAN checks: AntibodyForests results

Documentation:

Reference manual: AntibodyForests.html , AntibodyForests.pdf

Vignettes: AntibodyForests vignette: building and analyzing B-cell lineage trees from 10x sc-V(D)J seq data (source, R code)

Downloads:

Package source: AntibodyForests_1.1.0.tar.gz

Windows binaries: r-devel: AntibodyForests_1.1.0.zip, r-release: AntibodyForests_1.1.0.zip, r-oldrel: AntibodyForests_1.1.0.zip

macOS binaries: r-release (arm64): AntibodyForests_1.1.0.tgz, r-oldrel (arm64): AntibodyForests_1.1.0.tgz, r-release (x86_64): AntibodyForests_1.1.0.tgz, r-oldrel (x86_64): not available

Old sources: AntibodyForests archive

Linking:

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