B Cell Receptor Phylogenetics Toolkit
S4 class defining a clone in Dowser
Deprecated! Please use findSwitches instead.
buildClonalGermline Determine consensus clone sequence and create ge...
buildGermline reconstruct germline segments from alignment data
Wrapper to build IgPhyML trees and infer intermediate nodes
Wrapper for alakazam::buildPhylipLineage
Wrapper for phangorn::optim.pml
Wrapper for phangorn::pratchet
Wrapper to build RAxML-ng trees and infer intermediate nodes
Finds the Robinson-Fould's cluster distance between phylogenies.
Collapse internal nodes with the same predicted sequence
Get a color palette for a predefined set of trait values
Condense a set of equally parsimonious node labels into a single tree
Run date randomization test for temporal signal on a set of trees.
createGermlines Determine consensus clone sequence and create germline...
Write a fasta file of sequences readFasta reads a fasta file
downsampleClone Down-sample clone to maximum tip/switch ratio
dowser: B Cell Receptor Phylogenetics Toolkit
The dowser package
Exports the phylogentic trees from the airrClone object
Create a bootstrap distribution for clone sequence alignments, and est...
Generate an ordered list of airrClone objects for lineage construction
Return all tip and internal node sequences
Creates a bootstrap distribution for clone sequence alignments, and re...
Get divergence from root of tree for each tip
getGermline get germline segment from specified receptor and segment
Return IMGT gapped sequence of specified tree node
Get a color palette for a predefined set of trait values. 'Germline' d...
Deprecated! Use getNodeSeq
#' Deprecated! Use resolveLightChains
Get the tip labels as part of a clade defined by an internal node
Estimate lineage tree topologies, branch lengths, and internal node st...
Generate a airrClone object for lineage construction
Make a parsimony model file
maskCodons Masks codons split by insertions
maskSequences Mask codons split by insertions in V gene
Plot a tree with colored internal node labels using ggtree
Read a fasta file into a list of sequences readFasta reads a fasta f...
readIMGT read in IMGT database
Read in all trees from a lineages file
Read in a parsimony model file
Do IgPhyML maximum parsimony reconstruction
Reroot phylogenetic tree to have its germline sequence at a zero-lengt...
Define subgroups within clones based on light chain rearrangements
Resolve polytomies to have the minimum number of single timepoint clad...
Run correlationTest, based on https://doi.org/10.1111/2041-210X.12466
Scale branch lengths to represent either mutations or mutations per si...
stitchRegions Similar to stitchVDJ but with segment IDs instead of nul...
stitchVDJ combines germline gene segments to a single string
Performs PS (parsimony score) test on switch data
Performs SC (switch count) test on switch data
Performs SP (switch proportion) test on switch data
Simple function for plotting a lot of trees into a pdf
Write the sequences used in tree building to a fasta format. If there ...
Write lineage file for IgPhyML use
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>.