The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

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

Linking:

Please use the canonical form https://CRAN.R-project.org/package=ClusTCR2 to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.