Package: ClusTCR2
Title: Identifying Similar T Cell Receptor Hyper-Variable Sequences
        with 'ClusTCR2'
Version: 1.7.3.01
Date: 2024-05-15
Authors@R: c(person("Kerry A.", "Mullan", role = c("aut","cre"),
                     email = "Kerry.Mullan@uantwerpen.be"),
              person("Sebastiaan", "Valkiers", role = c("aut","ctb")),
              person("Kris", "Laukens", role = c("aut","ctb")),
              person("Pieter", "Meysman", role = c("aut","ctb"),
                     email = ""))
Author: Kerry A. Mullan [aut, cre], Sebastiaan Valkiers [aut, ctb],
        Kris Laukens [aut, ctb], Pieter Meysman [aut, ctb]
Description: 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>.
Maintainer: Kerry A. Mullan <Kerry.Mullan@uantwerpen.be>
License: GPL (>= 3)
Encoding: UTF-8
RoxygenNote: 7.3.1
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Config/testthat/edition: 3
Imports: DescTools, ggplot2, ggseqlogo, network, plyr, RColorBrewer,
        stringr, scales, sna, VLF
biocViews: GeneTarget, SingleCell
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2026-07-02 05:41:50 UTC; root
Repository: https://cran.r-universe.dev
Date/Publication: 2024-05-17 02:36:54 UTC
RemoteUrl: https://github.com/cran/ClusTCR2
RemoteRef: HEAD
RemoteSha: 712bcc780c7b33ba862aea979219ba986a5f4b0b