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 has 6 primary functions:

  1. Reconstruct clonal germline sequences.
  2. Build B cell lineage trees using multiple methods, such as maximum parsimony, maximum likelihood, and IgPhyML.
  3. Reconstruct intermediate sequences within lineage trees using different methods.
  4. Create publication-quality lineage tree plots.
  5. Analyze trees to detect ongoing B cell evolution over time.
  6. Understand B cell migration and differentiation.

What’s a dowser?

Documentation and tutorials

Full documentation, including tutorials and vignettes: Dowser ReadTheDocs site

For AI assistants/LLMs and other automated agents: llms.txt is a short curated index of Dowser’s documentation, and llms-full.txt concatenates the entire documentation corpus (every vignette and function reference page) into one file.

Citation

If you use Dowser in published research, please cite:

Hoehn K, Pybus O, Kleinstein S (2022). Phylogenetic analysis of migration, differentiation, and class switching in B cells. PLoS Computational Biology. https://doi.org/10.1371/journal.pcbi.1009885

Please also run citation("dowser") in R for the complete, feature-specific list — additional citations apply if you used the correlationTest measurable evolution test, built paired heavy/light chain trees, or used IgPhyML for tree building.

Contact

If you need help or have any questions, please contact the Immcantation Group.

If you have discovered a bug or have a feature request, you can open an issue using the issue tracker.

To receive alerts about Immcantation releases, news, events, and tutorials, join the Immcantation News Google Group. Membership settings can be adjusted to change the frequency of email updates.

Dependencies

Depends: ggplot2
Imports: airr, alakazam, ape, coda, dplyr, ggtree, graphics, gridExtra, markdown, methods, phangorn, phylotate, RColorBrewer, rlang, shazam, stats, stringr, tidyselect, tidyr, utils, pwalign, treeio, jsonlite
Suggests: knitr, rmarkdown, testthat, BiocManager

Authors

Kenneth Hoehn (aut, cre)
Cole Jensen (aut)
Jessie Fielding (aut)
Hunter Melton (aut)
Susanna Marquez (ctb)
Jason Vander Heiden (ctb)
Erick Matsen (ctb)
Steven Kleinstein (aut, cph)

Citing

To cite the dowser package in publications, please use

Hoehn K, Pybus O, Kleinstein S (2022). “Phylogenetic analysis of migration, differentiation, and class switching in B cells.” PLoS Computational Biology. doi:10.1371/journal.pcbi.1009885 https://doi.org/10.1371/journal.pcbi.1009885, https://doi.org/10.1371/journal.pcbi.1009885.

If you use the correlationTest function for measurable evolution, please also cite

Hoehn K, Turner J, Miller F, Jiang R, Ellebedy A, Pybus O, Kleinstein S (2021). “Human B cell lineages associated with germinal centers following influenza vaccination are measurably evolving.” eLife. doi:10.7554/eLife.70873 https://doi.org/10.7554/eLife.70873, https://elifesciences.org/articles/70873.

If you construct paired heavy and light chain trees, please also cite

Jensen C, Sumner J, Kleinstein S, Hoehn K (2024). “Inferring B Cell Phylogenies from Paired H and L Chain BCR Sequences with Dowser.” The Journal of Immunology. doi:10.4049/jimmunol.2300851 https://doi.org/10.4049/jimmunol.2300851, https://doi.org/10.4049/jimmunol.2300851.

If you additionally use IgPhyML for building trees please also cite

Hoehn K, Van der Heiden J, Zhou J, Lunter G, Pybus O, Kleinstein S (2019). “Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination.” PNAS. doi:10.1073/pnas.1906020116 https://doi.org/10.1073/pnas.1906020116, https://doi.org/10.1073/pnas.1906020116.

License

AGPL-3