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:
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')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 6 months agofrom:712bcc780c. Checks:OK: 2. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Oct 14 2024 |
R-4.5-linux | OK | Oct 14 2024 |
Exports:ClusTCRClusTCR_Largeggnet2mcl_clustermcl_cluster_largeMotif_from_cluster_filemotif_plotmotif_plot_largenetplot_ClusTCR2
Dependencies:askpassbootcellrangerclassclicodacolorspacecpp11crayoncurldata.tableDescToolse1071Exactexpmfansifarverggplot2ggseqlogogldgluegtablehmshttrisobandjsonlitelabelinglatticelifecyclelmommagrittrMASSMatrixmgcvmimemunsellmvtnormnetworknlmeopensslpillarpkgconfigplyrprettyunitsprogressproxyR6RColorBrewerRcppreadxlrematchrlangrootSolverstudioapiscalessnastatnet.commonstringistringrsystibbleutf8vctrsviridisLiteVLFwithr