Package: dowser
Type: Package
Version: 2.3
Date: 2024-10-21
Authors@R: c(person("Kenneth", "Hoehn", role=c("aut", "cre"),
                    email="kenneth.b.hoehn@dartmouth.edu"),
             person("Cole", "Jensen", role=c("ctb"),
                    email="cole.jensen@yale.edu"),
             person("Susanna", "Marquez", role=c("ctb"),
                    email="susanna.marquez@yale.edu"),
             person("Jason", "Vander Heiden", role=c("ctb"),
                    email="jason.vanderheiden@gmail.com"),
             person("Steven", "Kleinstein", role=c("aut", "cph"),
                    email="steven.kleinstein@yale.edu"))
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://bitbucket.org/kleinstein/dowser/issues
LazyData: true
BuildVignettes: true
VignetteBuilder: knitr
Encoding: UTF-8
Depends: R (>= 4.0), ggplot2 (>= 3.4.0)
biocViews:
Imports: airr, alakazam (>= 1.1.0), ape (>= 5.6), Biostrings, dplyr (>=
        1.0), ggtree, graphics, gridExtra, markdown, methods, phangorn
        (>= 2.7.1), phylotate, RColorBrewer, rlang, shazam (>= 1.1.1),
        stats, stringr, tidyselect, tidyr, utils
Suggests: knitr, rmarkdown, testthat, pwalign
RoxygenNote: 7.3.2
Collate: 'Data.R' 'Dowser.R' 'Clones.R' 'Classes.R' 'Plotting.R'
        'Germlines.R' 'Statistics.R' 'TreeFunctions.R' 'zzz.R'
NeedsCompilation: no
Packaged: 2024-10-22 00:09:02 UTC; kenneth
Author: Kenneth Hoehn [aut, cre],
  Cole Jensen [ctb],
  Susanna Marquez [ctb],
  Jason Vander Heiden [ctb],
  Steven Kleinstein [aut, cph]
Maintainer: Kenneth Hoehn <kenneth.b.hoehn@dartmouth.edu>
Repository: CRAN
Date/Publication: 2024-10-22 17:10:07 UTC
Built: R 4.5.0; ; 2025-01-31 06:40:33 UTC; unix
