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: | 2.3 |
|---|---|
| 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 |
Documentation:
Downloads:
Linking:
Please use the canonical formhttps://CRAN.R-project.org/package=dowserto link to this page.