B Cell Receptor Phylogenetics Toolkit
S4 class defining a clone in Dowser
Deprecated! Please use findSwitches instead.
Read in a directory from a BEAST run. Runs treeannotator and loganalys...
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.
Compare divergence along a tree in terms of mutations (sum of branches...
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.
Takes an airr clone object and returns BEAST2 Alignment xml of the seq...
Takes an airr clone object and returns BEAST2 XML to set a height prio...
Takes an airr clone object and returns BEAST2 XML to set a maximum hei...
Takes an airr clone object and returns BEAST2 XML for MRCA prior of th...
Takes an airr clone object and returns BEAST2 XML for MRCA prior of th...
Takes an airr clone object and returns BEAST2 rootfreqs xml of the ger...
Takes an airr clone object and tree and returns BEAST2 XML for setting...
Takes an airr clone object and returns BEAST2 XML for a trait/traitSet...
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 phylogenetic 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
Make data frames for Bayesian skyline plots
#' Deprecated! Use resolveLightChains
Get the tip labels as part of a clade defined by an internal node
Estimate time trees by running BEAST on each clone Applies XML `templa...
Iteratively resume getTimeTrees until convergence, as defined by all p...
Estimate lineage tree topologies, branch lengths, and internal node st...
Generate a airrClone object for lineage construction
Make a parsimony model file
get values for Bayesian Skyline plot
maskCodons Masks codons split by insertions
maskSequences Mask codons split by insertions in V gene
Simple function for plotting Bayesian skyline plots
Plot a tree with colored internal node labels using ggtree
Reads in a BEAST output directory
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
sampleCloneMultiGroup Down-sample clone to specified size with one o...
sampleClones Down-sample clones to specified size
Scale branch lengths to represent either mutations or mutations per si...
stitchRegions Similar to stitchVDJ but with segment IDs instead of nuc...
stitchVDJ combines germline gene segments to a single string
Check whether sequences have in-frame premature stop codons (PTCs)
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
Takes an airr clone object and template and writes a BEAST2 XML file
Wrapper to write multiple clones to XML files
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>.