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 (2020) <doi:10.1101/2020.05.30.124446>, Hoehn et al (2021) <doi:10.1101/2021.01.06.425648>.

Version: 0.1.0
Depends: R (≥ 3.1.2), ggplot2 (≥ 3.2.0)
Imports: alakazam (≥ 1.1.0), ape (≥ 5.5), Biostrings, dplyr (≥ 0.8.1), ggtree, graphics, gridExtra, markdown, methods, phangorn (≥ 2.7.1), phylotate, RColorBrewer, rlang, shazam (≥ 1.1.0), stats, stringr, tidyselect, tidyr, utils
Suggests: knitr, rmarkdown, testthat
Published: 2021-07-22
Author: Kenneth Hoehn [aut, cre], Susanna Marquez [ctb], Jason Vander Heiden [ctb], Steven Kleinstein [aut, cph]
Maintainer: Kenneth Hoehn <kenneth.hoehn at yale.edu>
BugReports: https://bitbucket.org/kleinstein/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.pdf
Vignettes: Trees
Germlines
Plots
Quickstart
Sequences

Downloads:

Package source: dowser_0.1.0.tar.gz
Windows binaries: r-devel: dowser_0.1.0.zip, r-release: dowser_0.1.0.zip, r-oldrel: not available
macOS binaries: r-release (arm64): dowser_0.1.0.tgz, r-release (x86_64): dowser_0.1.0.tgz, r-oldrel: not available

Linking:

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