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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 |
| 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_2.2.0.tar.gz |
| Windows binaries: | r-devel: dowser_2.2.0.zip, r-release: dowser_2.2.0.zip, r-oldrel: dowser_2.2.0.zip |
| 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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