ExampleMixedClones

A small example database subset from Turner, J. S. et al. Human germinal centres 
engage memory and naive B cells after influenza vaccination. Nature 586, 127–132 (2020).

datasets

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>.

Kenneth Hoehn

dowser

B Cell Receptor Phylogenetics Toolkit

Cole Jensen

Susanna Marquez

Jason Vander Heiden

Steven Kleinstein

ExampleMixedClones function

A data.frame with the following Change-O style columns:<ul>
<li><code>clone_id</code>: Clonal cluster</li>
<li><code>data</code>: List of airrClone objects</li>
<li><code>locus</code>: Locus identifier.</li>
<li><code>seqs</code>: Number of sequences</li>
<li><code>igphyml_partitioned_trees</code>: IgPhyML partitioned tree</li>
<li><code>raxml_partitioned_trees</code>: RAxML partitioned tree</li>
</ul>

Format

Example Multiple Partition Trees — ExampleMixedClones

Example Multiple Partition Trees

ExampleMixedClones: Example Multiple Partition Trees

Description

Usage

Arguments

Format