Package: dowser
Type: Package
Version: 2.4.2.999
Date: 2026-06-17
Authors@R: c(
    person("Kenneth", "Hoehn", email = "kenneth.b.hoehn@dartmouth.edu", role = c("aut", "cre")),
    person("Cole", "Jensen", email = "cole.jensen@yale.edu", role = "aut"),
    person("Jessie", "Fielding", email = "jessie.jo.fielding@dartmouth.edu", role = "aut"),
    person("Hunter", "Melton", email = "hunter.j.melton@dartmouth.edu", role = "aut"),
    person("Susanna", "Marquez", email = "susanna.marquez@yale.edu", role = "ctb"),
    person("Jason", "Vander Heiden", email = "jason.vanderheiden@gmail.com", role = "ctb"),
    person("Erick", "Matsen", role = "ctb"),
    person("Steven", "Kleinstein", email = "steven.kleinstein@yale.edu", role = c("aut", "cph"))
  )
Title: B Cell Receptor Phylogenetics Toolkit
Description: Provides a set of functions for inferring, visualizing,
        and analyzing B cell phylogenetic trees. Provides methods to 1)
        reconstruct unmutated ancestral sequences, 2) build B cell
        phylogenetic trees using multiple methods, 3) visualize trees
        with metadata at the tips, 4) reconstruct intermediate
        sequences, 5) detect biased ancestor-descendant relationships
        among metadata types Workflow examples available at
        documentation site (see URL). Citations: Hoehn et al (2022)
        <doi:10.1371/journal.pcbi.1009885>, Hoehn et al (2021)
        <doi:10.1101/2021.01.06.425648>.
License: AGPL-3
URL: https://dowser.readthedocs.io
BugReports: https://github.com/immcantation/dowser/issues
LazyData: true
BuildVignettes: true
VignetteBuilder: knitr
Encoding: UTF-8
Depends: R (>= 4.4), ggplot2 (>= 3.4.0)
biocViews:
Imports: airr, alakazam (>= 1.1.0), ape (>= 5.6), dplyr (>= 1.0),
        ggtree, graphics, gridExtra, markdown, methods, phangorn (>=
        2.7.1), phylotate, RColorBrewer, rlang, shazam (>= 1.1.1),
        stats, stringr, tidyselect, tidyr, utils, pwalign, treeio,
        jsonlite
Suggests: knitr, rmarkdown, testthat, BiocManager
RoxygenNote: 7.3.3
Collate: 'Data.R' 'Dowser.R' 'Clones.R' 'Classes.R' 'Plotting.R'
        'Germlines.R' 'Statistics.R' 'TreeFunctions.R'
        'TimeTreesFunctions.R' 'zzz.R'
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libbz2-dev libicu-dev
        liblzma-dev libpng-dev libuv1-dev libxml2-dev libx11-dev
        xz-utils zlib1g-dev
Repository: https://immcantation.r-universe.dev
Date/Publication: 2026-06-18 18:33:08 UTC
RemoteUrl: https://github.com/immcantation/dowser
RemoteRef: HEAD
RemoteSha: 6513fbf56a5ec5246d12dd4d549f6b1c64423a5d
NeedsCompilation: no
Packaged: 2026-06-18 19:34:47 UTC; root
Author: Kenneth Hoehn [aut, cre],
  Cole Jensen [aut],
  Jessie Fielding [aut],
  Hunter Melton [aut],
  Susanna Marquez [ctb],
  Jason Vander Heiden [ctb],
  Erick Matsen [ctb],
  Steven Kleinstein [aut, cph]
Maintainer: Kenneth Hoehn <kenneth.b.hoehn@dartmouth.edu>