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: | 2.3 |
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 |
Suggests: | knitr, rmarkdown, testthat, pwalign |
Published: | 2024-10-22 |
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 dartmouth.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 |
Package source: | dowser_2.3.tar.gz |
Windows binaries: | r-devel: dowser_2.3.zip, r-release: dowser_2.3.zip, r-oldrel: dowser_2.3.zip |
macOS binaries: | r-release (arm64): dowser_2.3.tgz, r-oldrel (arm64): dowser_2.3.tgz, r-release (x86_64): dowser_2.3.tgz, r-oldrel (x86_64): dowser_2.3.tgz |
Old sources: | dowser archive |
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