Dowser¶

Dowser is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq). Dowser provides a set of tools for performing phylogenetic analysis on B cell receptor repertoires. It supports building and visualizing trees using multiple methods, and implements statistical tests for discrete trait analysis of B cell migration, differentiation, and isotype switching.

Dowser is released under the AGPL-3 license.

For detailed instructions on usage, check out the Dowser documentation site

Notice¶

Dowser isn’t officially released yet, so please let us know if you’re planning to publish anything using it. All features are still in active development and will likely change in the near future. Feedback is be greatly appreciated.

Dependencies¶

Depends: ggplot2
Imports: alakazam, ape, Biostrings, dplyr, ggtree, graphics, gridExtra, markdown, methods, phangorn, phylotate, RColorBrewer, rlang, shazam, stats, stringr, tidyselect, tidyr, utils
Suggests: knitr, rmarkdown, testthat

Authors¶

Kenneth Hoehn (aut, cre)
Susanna Marquez (ctb)
Jason Vander Heiden (ctb)
Steven Kleinstein (aut, cph)

Citing¶

To cite the dowser package in publications, please use:

Hoehn K, Pybus O, Kleinstein S (2020). “Phylogenetic analysis of migration, differentiation, and class switching in B cells.” bioRxiv. doi: 10.1101/2020.05.30.124446 (URL: https://doi.org/10.1101/2020.05.30.124446), .

A BibTeX entry for LaTeX users is

@Article{, style = {citation}, title = {Phylogenetic analysis of migration, differentiation, and class switching in B cells.}, author = {Kenneth B. Hoehn and Oliver G. Pybus and Steven H. Kleinstein}, year = {2020}, journal = {bioRxiv}, url = {https://doi.org/10.1101/2020.05.30.124446}, doi = {10.1101/2020.05.30.124446}, }

License¶

AGPL-3