ClusTCR_Large

Creates ClusTCR matrix
This function identifies similar CDR3 amino acid sequences based on the same length and V_gene

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

ClusTCR_Large function

<dl><dt>my_file</dt>
<dd>uploaded file with junction_aa (CD3 sequences), variable gene.</dd>
<dt>allele</dt>
<dd>The allele, if present as *00 will be removed if the user requires it.</dd>
<dt>v_gene</dt>
<dd>Variable gene column name</dd></dl>

Arguments

Creates ClusTCR matrix
This function identifies similar CDR3 amino acid sequences based on the same length and V_gene — ClusTCR_Large

<dl>

<dt>my_file</dt>
<dd>uploaded file with junction_aa (CD3 sequences), variable gene.</dd>


<dt>allele</dt>
<dd>The allele, if present as *00 will be removed if the user requires it.</dd>


<dt>v_gene</dt>
<dd>Variable gene column name</dd>

</dl>

ClusTCR_Large: Creates ClusTCR matrix This function identifies similar CDR3 amino acid sequences based on the same length and V_gene

Description

Usage

Value

Arguments