Package: AntibodyForests
Title: Delineating Inter- And Intra-Antibody Repertoire Evolution
Version: 1.1.0
Authors@R: c(
    person("Daphne", "van Ginneken", email = "daphne.v.ginneken@gmail.com", role = c("aut", "cre")),
    person("Alexander", "Yermanos", role = "aut"),
    person("Valentijn", "Tromp", role = "aut"),
    person("Tudor-Stefan", "Cotet", role = "ctb")
  )
Maintainer: Daphne van Ginneken <daphne.v.ginneken@gmail.com>
Description: 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.
License: GPL-2
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
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.2
NeedsCompilation: no
Packaged: 2025-07-17 13:28:41 UTC; dginneke
Author: Daphne van Ginneken [aut, cre],
  Alexander Yermanos [aut],
  Valentijn Tromp [aut],
  Tudor-Stefan Cotet [ctb]
Repository: CRAN
Date/Publication: 2025-07-17 15:30:02 UTC
Built: R 4.5.3; ; 2026-07-08 04:18:22 UTC; windows
