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:
- Reconstruct clonal germline sequences.
- Build B cell lineage trees using multiple methods, such as maximum parsimony, maximum likelihood, and IgPhyML.
- Reconstruct intermediate sequences within lineage trees using different methods.
- Create publication-quality lineage tree plots.
- Analyze trees to detect ongoing B cell evolution over time.
- Understand B cell migration and differentiation.
Imports: alakazam, ape, Biostrings, dplyr, ggtree, graphics, gridExtra, markdown, methods, phangorn, phylotate, RColorBrewer, rlang, shazam, stats, stringr, tidyselect, tidyr, utils
Suggests: knitr, rmarkdown, testthat
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 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.