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

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>.

Version:	1.7.3.01
Imports:	DescTools, ggplot2, ggseqlogo, network, plyr, RColorBrewer, stringr, scales, sna, VLF
Suggests:	knitr, rmarkdown, testthat (≥ 3.0.0)
Published:	2024-05-16
DOI:	10.32614/CRAN.package.ClusTCR2
Author:	Kerry A. Mullan [aut, cre], Sebastiaan Valkiers [aut, ctb], Kris Laukens [aut, ctb], Pieter Meysman [aut, ctb]
Maintainer:	Kerry A. Mullan <Kerry.Mullan at uantwerpen.be>
License:	GPL (≥ 3)
NeedsCompilation:	no
CRAN checks:	ClusTCR2 results

Documentation:

Reference manual:	ClusTCR2.pdf
Vignettes:	ClusTCR2

Downloads:

Package source:	ClusTCR2_1.7.3.01.tar.gz
Windows binaries:	r-devel: ClusTCR2_1.7.3.01.zip, r-release: ClusTCR2_1.7.3.01.zip, r-oldrel: ClusTCR2_1.7.3.01.zip
macOS binaries:	r-release (arm64): ClusTCR2_1.7.3.01.tgz, r-oldrel (arm64): ClusTCR2_1.7.3.01.tgz, r-release (x86_64): ClusTCR2_1.7.3.01.tgz, r-oldrel (x86_64): ClusTCR2_1.7.3.01.tgz

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