Package: ClusTCR2 1.7.3.01

Kerry A. Mullan

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>.

Authors:Kerry A. Mullan [aut, cre], Sebastiaan Valkiers [aut, ctb], Kris Laukens [aut, ctb], Pieter Meysman [aut, ctb]

ClusTCR2_1.7.3.01.tar.gz
ClusTCR2_1.7.3.01.tar.gz(r-4.5-noble)ClusTCR2_1.7.3.01.tar.gz(r-4.4-noble)
ClusTCR2_1.7.3.01.tgz(r-4.4-emscripten)ClusTCR2_1.7.3.01.tgz(r-4.3-emscripten)
ClusTCR2.pdf |ClusTCR2.html
ClusTCR2/json (API)

# Install 'ClusTCR2' in R:
install.packages('ClusTCR2', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

genetargetsinglecell

2.00 score 1 scripts 153 downloads 9 exports 66 dependencies

Last updated 6 months agofrom:712bcc780c. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 14 2024
R-4.5-linuxOKOct 14 2024

Exports:ClusTCRClusTCR_Largeggnet2mcl_clustermcl_cluster_largeMotif_from_cluster_filemotif_plotmotif_plot_largenetplot_ClusTCR2

Dependencies:askpassbootcellrangerclassclicodacolorspacecpp11crayoncurldata.tableDescToolse1071Exactexpmfansifarverggplot2ggseqlogogldgluegtablehmshttrisobandjsonlitelabelinglatticelifecyclelmommagrittrMASSMatrixmgcvmimemunsellmvtnormnetworknlmeopensslpillarpkgconfigplyrprettyunitsprogressproxyR6RColorBrewerRcppreadxlrematchrlangrootSolverstudioapiscalessnastatnet.commonstringistringrsystibbleutf8vctrsviridisLiteVLFwithr

ClusTCR2

Rendered fromClusTCR2.Rmdusingknitr::rmarkdownon Oct 14 2024.

Last update: 2024-05-17
Started: 2024-05-17