dowser: B Cell Receptor Phylogenetics Toolkit (original) (raw)

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:	2.4.0
Depends:	R (≥ 4.0), ggplot2 (≥ 3.4.0)
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, treeio
Suggests:	knitr, rmarkdown, testthat, pwalign, BiocManager
Published:	2025-10-14
DOI:	10.32614/CRAN.package.dowser
Author:	Kenneth Hoehn [aut, cre], Cole Jensen [aut], Jessie Fielding [aut], Hunter Melton [aut], Susanna Marquez [ctb], Jason Vander Heiden [ctb], Steven Kleinstein [aut, cph]
Maintainer:	Kenneth Hoehn <kenneth.b.hoehn at dartmouth.edu>
BugReports:	https://github.com/immcantation/dowser/issues
License:	AGPL-3
URL:	https://dowser.readthedocs.io
NeedsCompilation:	no
Citation:	dowser citation info
Materials:	README, NEWS
CRAN checks:	dowser results

Documentation:

Reference manual:	dowser.html , <dowser.pdf>
Vignettes:	Build Time Trees Using TyCHE and BEAST (source, R code) Build Lineage Trees (source, R code) Discrete Trait Analysis (source, R code) Reconstruct Clonal Germlines (source, R code) Measurable evolution (source, R code) Using data from non-B cells (source, R code) Plotting Lineage Trees (source, R code) Quickstart (source, R code) Building trees with paired heavy and light chain data (source, R code) Reconstruct Intermediate Sequences (source, R code)

Reference manual:

dowser.html , <dowser.pdf>

Vignettes:

Build Time Trees Using TyCHE and BEAST (source, R code) Build Lineage Trees (source, R code) Discrete Trait Analysis (source, R code) Reconstruct Clonal Germlines (source, R code) Measurable evolution (source, R code) Using data from non-B cells (source, R code) Plotting Lineage Trees (source, R code) Quickstart (source, R code) Building trees with paired heavy and light chain data (source, R code) Reconstruct Intermediate Sequences (source, R code)

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