The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.

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 (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:

Reference manual: dowser.pdf
Vignettes: Build Lineage Trees (source, R code)
Discrete Trait Analysis (source, R code)
Reconstruct Clonal Germlines (source, R code)
Measurable evolution (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)

Downloads:

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

Linking:

Please use the canonical form https://CRAN.R-project.org/package=dowser to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.