Motif_from_cluster_file

Code for plotting the Motif based on a specific CDR3 length and V gene (see netplot_ClusTCR2 for details).

Enhancing T cell receptor (TCR) sequence analysis, 'ClusTCR2', based on 'ClusTCR' python program, leverages Hamming distance to compare the complement-determining region three (CDR3) sequences for sequence similarity, variable gene (V gene) and length. The second step employs the Markov Cluster Algorithm to identify clusters within an undirected graph, providing a summary of amino acid motifs and matrix for generating network plots. Tailored for single-cell RNA-seq data with integrated TCR-seq information, 'ClusTCR2' is integrated into the Single Cell TCR and Expression Grouped Ontologies (STEGO) R application or 'STEGO.R'. See the two publications for more details. Sebastiaan Valkiers, Max Van Houcke, Kris Laukens, Pieter Meysman (2021) <doi:10.1093/bioinformatics/btab446>, Kerry A. Mullan, My Ha, Sebastiaan Valkiers, Nicky de Vrij, Benson Ogunjimi, Kris Laukens, Pieter Meysman (2023) <doi:10.1101/2023.09.27.559702>.

Kerry A. Mullan

ClusTCR2

Identifying Similar T Cell Receptor Hyper-Variable Sequences
with 'ClusTCR2'

Sebastiaan Valkiers

Kris Laukens

Pieter Meysman

Motif_from_cluster_file function

<dl><dt>ClusTCR</dt>
<dd>Cluster file produced from mcl_cluster.</dd>
<dt>Clust_selected</dt>
<dd>Select which cluster to review.</dd>
<dt>selected_cluster_column</dt>
<dd>Select the column "Clust_size_order" of the cluster ordered.</dd></dl>

Arguments

Code for plotting the Motif based on a specific CDR3 length and V gene (see netplot_ClusTCR2 for details). — Motif_from_cluster_file

<dl>

<dt>ClusTCR</dt>
<dd>Cluster file produced from mcl_cluster.</dd>


<dt>Clust_selected</dt>
<dd>Select which cluster to review.</dd>


<dt>selected_cluster_column</dt>
<dd>Select the column "Clust_size_order" of the cluster ordered.</dd>

</dl>

Motif_from_cluster_file: Code for plotting the Motif based on a specific CDR3 length and V gene (see netplot_ClusTCR2 for details).

Description

Usage

Value

Arguments