dowser: B Cell Receptor Phylogenetics Toolkit

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>.

Version: 2.2.0
Depends: R (≥ 4.0), ggplot2 (≥ 3.4.0)
Imports: 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
Published: 2024-05-09
DOI: 10.32614/CRAN.package.dowser
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 at>
License: AGPL-3
NeedsCompilation: no
Citation: dowser citation info
Materials: README NEWS
CRAN checks: dowser results


Reference manual: dowser.pdf
Vignettes: Build Lineage Trees
Discrete Trait Analysis
Reconstruct Clonal Germlines
Measurable evolution
Plotting Lineage Trees
Building trees with paired heavy and light chain data
Reconstruct Intermediate Sequences


Package source: dowser_2.2.0.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): dowser_2.2.0.tgz, r-oldrel (arm64): dowser_2.2.0.tgz, r-release (x86_64): dowser_2.2.0.tgz, r-oldrel (x86_64): dowser_2.2.0.tgz
Old sources: dowser archive


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