ExampleAirrTyCHE

A small example database from simble.

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

Jessie Fielding

Hunter Melton

Susanna Marquez

Jason Vander Heiden

Steven Kleinstein

ExampleAirrTyCHE function

A data.frame with the following AIRR style columns:<ul>
<li><code>sequence_id</code>: Sequence identifier</li>
<li><code>sequence_alignment</code>: IMGT-gapped observed sequence.</li>
<li><code>germline_alignment</code>: IMGT-gapped germline sequence.</li>
<li><code>v_call</code>: V region allele assignments.</li>
<li><code>d_call</code>: D region allele assignments.</li>
<li><code>j_call</code>: J region allele assignments.</li>
<li><code>junction</code>: Junction region sequence.</li>
<li><code>junction_length</code>: Length of the junction region in nucleotides.</li>
<li><code>np1_length</code>: Combined length of the N and P regions proximal
 to the V region.</li>
<li><code>np2_length</code>: Combined length of the N and P regions proximal
 to the J region.</li>
<li><code>sample_time</code>: Time point of the sample.</li>
<li><code>location</code>: Location of tissue from which the sample was taken.</li>
<li><code>clone_id</code>: Clonal group identifier.</li>
</ul>

Format

Example AIRR database for TyCHE — ExampleAirrTyCHE

Example AIRR database for TyCHE

ExampleAirrTyCHE: Example AIRR database for TyCHE

Description

Usage

Arguments

Format

References