{ "_id": "6a1e7a9a1d7bb097a0a64bc2", "Package": "ClusTCR2", "Title": "Identifying Similar T Cell Receptor Hyper-Variable Sequences\nwith 'ClusTCR2'", "Version": "1.7.3.01", "Date": "2024-05-15", "Authors@R": "c(person(\"Kerry A.\", \"Mullan\", role = c(\"aut\",\"cre\"),\nemail = \"Kerry.Mullan@uantwerpen.be\"),\nperson(\"Sebastiaan\", \"Valkiers\", role = c(\"aut\",\"ctb\")),\nperson(\"Kris\", \"Laukens\", role = c(\"aut\",\"ctb\")),\nperson(\"Pieter\", \"Meysman\", role = c(\"aut\",\"ctb\"),\nemail = \"\"))", "Author": "Kerry A. Mullan [aut, cre], Sebastiaan Valkiers [aut, ctb],\nKris Laukens [aut, ctb], Pieter Meysman [aut, ctb]", "Description": "Enhancing T cell receptor (TCR) sequence analysis,\n'ClusTCR2', based on 'ClusTCR' python program, leverages\nHamming distance to compare the complement-determining region\nthree (CDR3) sequences for sequence similarity, variable gene\n(V gene) and length. The second step employs the Markov Cluster\nAlgorithm to identify clusters within an undirected graph,\nproviding a summary of amino acid motifs and matrix for\ngenerating network plots. Tailored for single-cell RNA-seq data\nwith integrated TCR-seq information, 'ClusTCR2' is integrated\ninto the Single Cell TCR and Expression Grouped Ontologies\n(STEGO) R application or 'STEGO.R'. See the two publications\nfor more details. Sebastiaan Valkiers, Max Van Houcke, Kris\nLaukens, Pieter Meysman (2021)\n, Kerry A. Mullan, My Ha,\nSebastiaan Valkiers, Nicky de Vrij, Benson Ogunjimi, Kris\nLaukens, Pieter Meysman (2023) .", "Maintainer": "Kerry A. 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from ggnet's ggnet2 function", "topics": [ "ggnet2" ] }, { "page": "mcl_cluster", "title": "Create the files for labeling the linked clusters from ClusTCR_list_to_matrix function", "topics": [ "mcl_cluster" ] }, { "page": "mcl_cluster_large", "title": "Create the files for labeling the linked clusters from ClusTCR_list_to_matrix function", "topics": [ "mcl_cluster_large" ] }, { "page": "Motif_from_cluster_file", "title": "Code for plotting the Motif based on a specific CDR3 length and V gene (see netplot_ClusTCR2 for details).", "topics": [ "Motif_from_cluster_file" ] }, { "page": "motif_plot", "title": "Code for plotting the Motif based on a specific CDR3 length and V gene (see netplot_ClusTCR2 for ).", "topics": [ "motif_plot" ] }, { "page": "motif_plot_large", "title": "Code for plotting the Motif based on a specific CDR3 length and V gene (see netplot_ClusTCR2 for details).", "topics": [ "motif_plot_large" ] }, { "page": "netplot_ClusTCR2", "title": "Code for displaying the 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