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  "Title": "Multi-Modal Immune Repertoire Analytics for Immunotherapy and\nVaccine Design in R",
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  "Authors@R": "c(\nperson(\"Vadim I.\", \"Nazarov\", , \"support@immunomind.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-3659-2709\")),\nperson(\"Vasily O.\", \"Tsvetkov\", , role = \"aut\"),\nperson(\"Aleksandr A.\", \"Popov\", , role = \"aut\"),\nperson(\"Ivan\", \"Balashov\", , role = \"aut\")\n)",
  "Contact": "support@immunomind.com",
  "Description": "A comprehensive analytics framework for building\nreproducible pipelines on T-cell and B-cell immune receptor\nrepertoire data. Delivers multi-modal immune profiling (bulk,\nsingle-cell, CITE-seq/AbSeq, spatial, immunogenicity data),\nfeature engineering (ML-ready feature tables and matrices), and\nbiomarker discovery workflows (cohort comparisons, longitudinal\ntracking, repertoire similarity, enrichment). Provides a\nuser-friendly interface to widely used AIRR methods —\nclonality/diversity, V(D)J usage, similarity, annotation,\ntracking, and many more. Think Scanpy or Seurat, but for AIRR\ndata, a.k.a. Adaptive Immune Receptor Repertoire, VDJ-seq,\nRepSeq, or VDJ sequencing data. A successor to our previously\npublished \"tcR\" R package (Nazarov 2015).",
  "License": "Apache License (>= 2.0)",
  "URL": "https://immunomind.github.io/docs/,\nhttps://github.com/immunomind/immunarch/,\nhttps://immunarch.com/",
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  "Date/Publication": "2025-11-18 12:28:58 UTC",
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    "airr_clonality_prop",
    "airr_clonality_rank",
    "airr_desc_chains",
    "airr_desc_genes",
    "airr_desc_lengths",
    "airr_diversity_chao1",
    "airr_diversity_dxx",
    "airr_diversity_hill",
    "airr_diversity_index",
    "airr_diversity_pielou",
    "airr_diversity_shannon",
    "annotate_clonality_prop",
    "annotate_clonality_rank",
    "apply_asymm",
    "apply_symm",
    "bunch_translate",
    "coding",
    "cross_entropy",
    "dbAnnotate",
    "dbLoad",
    "entropy",
    "exclude",
    "fixVis",
    "gene_stats",
    "geneUsage",
    "geneUsageAnalysis",
    "get_genes",
    "get_immunarch_news",
    "getKmers",
    "immunr_dbscan",
    "immunr_hclust",
    "immunr_kmeans",
    "immunr_mds",
    "immunr_pca",
    "immunr_tsne",
    "inc_overlap",
    "include",
    "inframes",
    "interval",
    "js_div",
    "kl_div",
    "kmer_profile",
    "lessthan",
    "list_immunarch_news",
    "morethan",
    "noncoding",
    "outofframes",
    "public_matrix",
    "publicRepertoire",
    "publicRepertoireApply",
    "publicRepertoireFilter",
    "pubRep",
    "pubRepApply",
    "pubRepFilter",
    "pubRepStatistics",
    "repAlignLineage",
    "repClonalFamily",
    "repClonality",
    "repDiversity",
    "repExplore",
    "repFilter",
    "repGermline",
    "repLoad",
    "repOverlap",
    "repOverlapAnalysis",
    "repSample",
    "repSave",
    "repsim_intersection",
    "repsim_jaccard",
    "repSomaticHypermutation",
    "select_barcodes",
    "select_clusters",
    "seqCluster",
    "seqDist",
    "spectratype",
    "split_to_kmers",
    "top",
    "trackClonotypes",
    "vis",
    "vis_bar",
    "vis_box",
    "vis_circos",
    "vis_heatmap",
    "vis_heatmap2",
    "vis_hist",
    "vis_immunr_kmer_profile_main",
    "vis_seqlogo",
    "vis_textlogo"
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      "name": "AA_PROP",
      "title": "Tables with amino acid properties",
      "object": "aaproperties",
      "class": [
        "data.frame"
      ],
      "fields": [
        "amino.acid",
        "alpha",
        "beta",
        "charge",
        "core",
        "hydropathy",
        "pH",
        "polarity",
        "rim",
        "surface",
        "turn",
        "volume",
        "count",
        "strength",
        "disorder",
        "high_contact",
        "count"
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      "rows": 20,
      "table": true,
      "tojson": true
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    {
      "name": "ATCHLEY",
      "title": "Tables with amino acid properties",
      "object": "aaproperties",
      "class": [
        "data.frame"
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      "fields": [
        "amino.acid",
        "f1",
        "f2",
        "f3",
        "f4",
        "f5"
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      "rows": 20,
      "table": true,
      "tojson": true
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      "name": "bcrdata",
      "title": "BCR dataset",
      "object": "bcrdata",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "GENE_SEGMENTS",
      "title": "Gene segments table",
      "object": "genesegments",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
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        "alias",
        "species",
        "gene",
        "family_id",
        "segment_id",
        "allele_id",
        "reference_point",
        "sequence"
      ],
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      "tojson": true
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      "title": "Single chain immune repertoire dataset",
      "object": "immdata",
      "class": [
        "list"
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      "fields": [],
      "table": false,
      "tojson": true
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      "name": "KIDERA",
      "title": "Tables with amino acid properties",
      "object": "aaproperties",
      "class": [
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        "f1",
        "f2",
        "f3",
        "f4",
        "f5",
        "f6",
        "f7",
        "f8",
        "f9",
        "f10"
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      "table": true,
      "tojson": true
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      "page": "dot-quant_column_choice",
      "title": "Get a column's name using the input alias",
      "concept": [
        "utility_private"
      ],
      "topics": [
        ".quant_column_choice"
      ]
    },
    {
      "page": "aa_properties",
      "title": "Tables with amino acid properties",
      "concept": [
        "data"
      ],
      "topics": [
        "AA_PROP",
        "aa_prop",
        "aa_properties",
        "ATCHLEY",
        "atchley",
        "KIDERA",
        "kidera",
        "properties"
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    {
      "page": "aa_table",
      "title": "Amino acid / codon table",
      "concept": [
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        "aa_table",
        "AA_TABLE_REVERSED"
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    {
      "page": "add_class",
      "title": "Add a new class attribute",
      "concept": [
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      "topics": [
        "add_class"
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    {
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      "title": "Clonality - receptor overabundance statistics for immune repertoires",
      "concept": [
        "Clonality"
      ],
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        "airr_clonality",
        "airr_clonality_line",
        "airr_clonality_prop",
        "airr_clonality_rank"
      ]
    },
    {
      "page": "airr_desc",
      "title": "Compute key immune repertoire statistics",
      "concept": [
        "Key AIRR statistics"
      ],
      "topics": [
        "airr_desc",
        "airr_desc_chains",
        "airr_desc_genes",
        "airr_desc_lengths"
      ]
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    {
      "page": "airr_diversity",
      "title": "Diversity - estimating the heterogeneity of immune repertoires",
      "concept": [
        "Diversity"
      ],
      "topics": [
        "airr_diversity",
        "airr_diversity_chao1",
        "airr_diversity_dxx",
        "airr_diversity_hill",
        "airr_diversity_index",
        "airr_diversity_pielou",
        "airr_diversity_shannon"
      ]
    },
    {
      "page": "annotate_clonality",
      "title": "Annotate clonality - per-receptor labels for overabundance",
      "concept": [
        "Clonality"
      ],
      "topics": [
        "annotate_clonality",
        "annotate_clonality_prop",
        "annotate_clonality_rank"
      ]
    },
    {
      "page": "apply_symm",
      "title": "Apply function to each pair of data frames from a list.",
      "concept": [
        "utility_public"
      ],
      "topics": [
        "apply_asymm",
        "apply_symm"
      ]
    },
    {
      "page": "bcrdata",
      "title": "BCR dataset",
      "concept": [
        "data"
      ],
      "topics": [
        "bcrdata"
      ]
    },
    {
      "page": "bunch_translate",
      "title": "Nucleotide to amino acid sequence translation",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "bunch_translate",
        "translate_bunch"
      ]
    },
    {
      "page": "check_distribution",
      "title": "Check and normalise distributions",
      "concept": [
        "utility_private"
      ],
      "topics": [
        "check_distribution"
      ]
    },
    {
      "page": "coding",
      "title": "Filter out coding and non-coding clonotype sequences",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "coding",
        "inframes",
        "noncoding",
        "outofframes"
      ]
    },
    {
      "page": "dbAnnotate",
      "title": "Annotate clonotypes in immune repertoires using clonotype databases (e.g., VDJDB, McPAS)",
      "concept": [
        "annotation"
      ],
      "topics": [
        "dbAnnotate"
      ]
    },
    {
      "page": "dbLoad",
      "title": "Load clonotype databases such as VDJDB and McPAS into the R workspace",
      "concept": [
        "annotation"
      ],
      "topics": [
        "dbLoad"
      ]
    },
    {
      "page": "entropy",
      "title": "Information measures",
      "concept": [
        "utility_public"
      ],
      "topics": [
        "cross_entropy",
        "entropy",
        "js_div",
        "kl_div"
      ]
    },
    {
      "page": "fixVis",
      "title": "Manipulate ggplot plots and create publication-ready plots",
      "concept": [
        "fixvis"
      ],
      "topics": [
        "fixVis"
      ]
    },
    {
      "page": "gene_segments",
      "title": "Gene segments table",
      "concept": [
        "data"
      ],
      "topics": [
        "genes",
        "GENE_SEGMENTS",
        "gene_segments",
        "segments"
      ]
    },
    {
      "page": "gene_stats",
      "title": "WIP",
      "concept": [
        "data"
      ],
      "topics": [
        "gene_stats"
      ]
    },
    {
      "page": "geneUsage",
      "title": "Main function for estimation of V-gene and J-gene statistics",
      "concept": [
        "gene_usage"
      ],
      "topics": [
        "geneUsage",
        "get_aliases",
        "get_genes"
      ]
    },
    {
      "page": "geneUsageAnalysis",
      "title": "Post-analysis of V-gene and J-gene statistics: PCA, clustering, etc.",
      "concept": [
        "gene_usage"
      ],
      "topics": [
        "geneUsageAnalysis"
      ]
    },
    {
      "page": "get_immunarch_news",
      "title": "Get the Latest immunarch Update",
      "concept": [
        "migration_utility"
      ],
      "topics": [
        "get_immunarch_news"
      ]
    },
    {
      "page": "getKmers",
      "title": "Calculate the k-mer statistics of immune repertoires",
      "concept": [
        "k-mers"
      ],
      "topics": [
        "get.kmers",
        "getKmers",
        "makeKmerTable"
      ]
    },
    {
      "page": "group_from_metadata",
      "title": "Get a character vector of samples' groups from the input metadata file",
      "concept": [
        "utility_private"
      ],
      "topics": [
        "group_from_metadata"
      ]
    },
    {
      "page": "has_class",
      "title": "Check for the specific class",
      "concept": [
        "utility_private"
      ],
      "topics": [
        "has_class"
      ]
    },
    {
      "page": "immdata",
      "title": "Single chain immune repertoire dataset",
      "concept": [
        "data"
      ],
      "topics": [
        "immdata"
      ]
    },
    {
      "page": "immunarch_v1_updates",
      "title": "Get a list of package updates",
      "concept": [
        "migration_utility"
      ],
      "topics": [
        "immunarch_v1_updates"
      ]
    },
    {
      "page": "immunr_data_format",
      "title": "Specification of the data format used by immunarch dataframes",
      "concept": [
        "data"
      ],
      "topics": [
        "immunarch_data_format",
        "immunr_data_format"
      ]
    },
    {
      "page": "immunr_hclust",
      "title": "Clustering of objects or distance matrices",
      "concept": [
        "post_analysis"
      ],
      "topics": [
        "immunr_dbscan",
        "immunr_hclust",
        "immunr_kmeans"
      ]
    },
    {
      "page": "immunr_pca",
      "title": "Dimensionality reduction",
      "concept": [
        "post_analysis"
      ],
      "topics": [
        "immunr_mds",
        "immunr_pca",
        "immunr_tsne"
      ]
    },
    {
      "page": "inc_overlap",
      "title": "Incremental counting of repertoire similarity",
      "concept": [
        "overlap"
      ],
      "topics": [
        "inc_overlap"
      ]
    },
    {
      "page": "list_immunarch_news",
      "title": "List Available immunarch Updates",
      "concept": [
        "migration_utility"
      ],
      "topics": [
        "list_immunarch_news"
      ]
    },
    {
      "page": "matrixdiagcopy",
      "title": "Copy the upper matrix triangle to the lower one",
      "concept": [
        "utility_private"
      ],
      "topics": [
        "matrixdiagcopy"
      ]
    },
    {
      "page": "public_matrix",
      "title": "Get a matrix with public clonotype frequencies",
      "concept": [
        "pubrep"
      ],
      "topics": [
        "public_matrix"
      ]
    },
    {
      "page": "pubRep",
      "title": "Create a repertoire of public clonotypes",
      "concept": [
        "pubrep"
      ],
      "topics": [
        "publicRepertoire",
        "pubRep"
      ]
    },
    {
      "page": "pubRepApply",
      "title": "Apply transformations to public repertoires",
      "concept": [
        "pubrep"
      ],
      "topics": [
        "publicRepertoireApply",
        "pubRepApply"
      ]
    },
    {
      "page": "pubRepFilter",
      "title": "Filter out clonotypes from public repertoires",
      "concept": [
        "pubrep"
      ],
      "topics": [
        "publicRepertoireFilter",
        "pubRepFilter"
      ]
    },
    {
      "page": "pubRepStatistics",
      "title": "Statistics of number of public clonotypes for each possible combinations of repertoires",
      "concept": [
        "pubrep"
      ],
      "topics": [
        "pubRepStatistics"
      ]
    },
    {
      "page": "repAlignLineage",
      "title": "Aligns all sequences incliding germline within each clonal lineage within each cluster",
      "concept": [
        "align_lineage"
      ],
      "topics": [
        "repAlignLineage"
      ]
    },
    {
      "page": "repClonalFamily",
      "title": "Builds a phylogenetic tree using the sequences of a clonal lineage",
      "concept": [
        "phylip"
      ],
      "topics": [
        "repClonalFamily"
      ]
    },
    {
      "page": "repClonality",
      "title": "Clonality analysis of immune repertoires",
      "concept": [
        "clonality"
      ],
      "topics": [
        "clonal.prop",
        "clonality",
        "clonal_proportion",
        "clonal_space_homeostasis",
        "rare_proportion",
        "repClonality",
        "top_proportion"
      ]
    },
    {
      "page": "repDiversity",
      "title": "The main function for immune repertoire diversity estimation",
      "concept": [
        "diversity"
      ],
      "topics": [
        "chao1",
        "diversity_eco",
        "gini_coef",
        "gini_simpson",
        "hill_numbers",
        "inverse_simpson",
        "rarefaction",
        "repDiversity"
      ]
    },
    {
      "page": "repExplore",
      "title": "Main function for exploratory data analysis: compute the distribution of lengths, clones, etc.",
      "concept": [
        "explore"
      ],
      "topics": [
        "repExplore"
      ]
    },
    {
      "page": "repFilter",
      "title": "Main function for data filtering",
      "concept": [
        "filters"
      ],
      "topics": [
        "exclude",
        "include",
        "interval",
        "lessthan",
        "morethan",
        "repFilter"
      ]
    },
    {
      "page": "repGermline",
      "title": "Creates germlines for clonal lineages",
      "concept": [
        "germline"
      ],
      "topics": [
        "repGermline"
      ]
    },
    {
      "page": "repLoad",
      "title": "Load immune repertoire files into the R workspace",
      "concept": [
        "io"
      ],
      "topics": [
        "repLoad"
      ]
    },
    {
      "page": "repOverlap",
      "title": "Main function for public clonotype statistics calculations",
      "concept": [
        "overlap"
      ],
      "topics": [
        "repOverlap"
      ]
    },
    {
      "page": "repOverlapAnalysis",
      "title": "Post-analysis of public clonotype statistics: PCA, clustering, etc.",
      "concept": [
        "overlap"
      ],
      "topics": [
        "repOverlapAnalysis"
      ]
    },
    {
      "page": "repSample",
      "title": "Downsampling and resampling of immune repertoires",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "repSample"
      ]
    },
    {
      "page": "repSave",
      "title": "Save immune repertoires to the disk",
      "concept": [
        "io"
      ],
      "topics": [
        "repSave"
      ]
    },
    {
      "page": "repsim",
      "title": "Public indices - pairwise repertoire overlap",
      "concept": [
        "Repertoire similarity"
      ],
      "topics": [
        "repsim",
        "repsim_intersection",
        "repsim_jaccard"
      ]
    },
    {
      "page": "repSomaticHypermutation",
      "title": "Calculates number of mutations against the germline for each clonotype",
      "concept": [
        "somatic_hypermutation"
      ],
      "topics": [
        "repSomaticHypermutation"
      ]
    },
    {
      "page": "select_barcodes",
      "title": "Select specific clonotypes using barcodes from single-cell metadata",
      "concept": [
        "single_cell"
      ],
      "topics": [
        "select_barcodes"
      ]
    },
    {
      "page": "select_clusters",
      "title": "Split the immune repertoire data to clusters from single-cell barcodes",
      "concept": [
        "single_cell"
      ],
      "topics": [
        "select_clusters"
      ]
    },
    {
      "page": "seqCluster",
      "title": "Function for assigning clusters based on sequences similarity",
      "concept": [
        "seq_cluster"
      ],
      "topics": [
        "seqCluster"
      ]
    },
    {
      "page": "seqDist",
      "title": "Function for computing distance for sequences",
      "concept": [
        "distance"
      ],
      "topics": [
        "seqDist"
      ]
    },
    {
      "page": "set_pb",
      "title": "Set and update progress bars",
      "concept": [
        "utility_private"
      ],
      "topics": [
        "add_pb",
        "set_pb"
      ]
    },
    {
      "page": "spectratype",
      "title": "Immune repertoire spectratyping",
      "concept": [
        "vis"
      ],
      "topics": [
        "spectratype"
      ]
    },
    {
      "page": "split_to_kmers",
      "title": "Analysis immune repertoire kmer statistics: sequence profiles, etc.",
      "concept": [
        "k-mers"
      ],
      "topics": [
        "kmer_profile",
        "split_to_kmers"
      ]
    },
    {
      "page": "switch_type",
      "title": "Return a column's name",
      "concept": [
        "utility_private"
      ],
      "topics": [
        "process_col_argument",
        "switch_type"
      ]
    },
    {
      "page": "top",
      "title": "Get the N most abundant clonotypes",
      "concept": [
        "preprocessing"
      ],
      "topics": [
        "top"
      ]
    },
    {
      "page": "trackClonotypes",
      "title": "Track clonotypes across time and data points",
      "concept": [
        "dynamics"
      ],
      "topics": [
        "trackClonotypes"
      ]
    },
    {
      "page": "vis",
      "title": "One function to visualise them all",
      "topics": [
        "vis"
      ]
    },
    {
      "page": "vis_bar",
      "title": "Bar plots",
      "concept": [
        "vis"
      ],
      "topics": [
        "vis_bar"
      ]
    },
    {
      "page": "vis_box",
      "title": "Flexible box-plots for visualisation of distributions",
      "concept": [
        "vis"
      ],
      "topics": [
        "vis_box"
      ]
    },
    {
      "page": "vis_circos",
      "title": "Visualisation of matrices using circos plots",
      "concept": [
        "vis"
      ],
      "topics": [
        "vis_circos"
      ]
    },
    {
      "page": "vis_heatmap",
      "title": "Visualisation of matrices and data frames using ggplo2-based heatmaps",
      "concept": [
        "vis"
      ],
      "topics": [
        "vis_heatmap"
      ]
    },
    {
      "page": "vis_heatmap2",
      "title": "Visualisation of matrices using pheatmap-based heatmaps",
      "concept": [
        "vis"
      ],
      "topics": [
        "vis_heatmap2"
      ]
    },
    {
      "page": "vis_hist",
      "title": "Visualisation of distributions using histograms",
      "concept": [
        "vis"
      ],
      "topics": [
        "vis_hist"
      ]
    },
    {
      "page": "vis_immunr_kmer_profile_main",
      "title": "Visualise kmer profiles",
      "concept": [
        "kmers"
      ],
      "topics": [
        "vis_immunr_kmer_profile_main"
      ]
    },
    {
      "page": "vis_public_clonotypes",
      "title": "Visualisation of public clonotypes",
      "concept": [
        "pubrep"
      ],
      "topics": [
        "vis_public_clonotypes"
      ]
    },
    {
      "page": "vis_public_frequencies",
      "title": "Public repertoire visualisation",
      "concept": [
        "pubrep"
      ],
      "topics": [
        "vis_public_frequencies"
      ]
    },
    {
      "page": "vis_textlogo",
      "title": "Sequence logo plots for amino acid profiles.",
      "concept": [
        "kmers"
      ],
      "topics": [
        "vis_seqlogo",
        "vis_textlogo"
      ]
    },
    {
      "page": "vis.clonal_family",
      "title": "Visualise clonal family tree: wrapper for calling on the entire repClonalFamily output",
      "concept": [
        "phylip"
      ],
      "topics": [
        "vis.clonal_family"
      ]
    },
    {
      "page": "vis.clonal_family_tree",
      "title": "Visualise clonal family tree",
      "concept": [
        "phylip"
      ],
      "topics": [
        "vis.clonal_family_tree"
      ]
    },
    {
      "page": "vis.immunr_chao1",
      "title": "Visualise diversity.",
      "concept": [
        "diversity"
      ],
      "topics": [
        "vis.immunr_chao1",
        "vis.immunr_div",
        "vis.immunr_dxx",
        "vis.immunr_ginisimp",
        "vis.immunr_hill",
        "vis.immunr_invsimp",
        "vis.immunr_rarefaction"
      ]
    },
    {
      "page": "vis.immunr_clonal_prop",
      "title": "Visualise results of the clonality analysis",
      "concept": [
        "clonality"
      ],
      "topics": [
        "vis.immunr_clonal_prop",
        "vis.immunr_homeo",
        "vis.immunr_tail_prop",
        "vis.immunr_top_prop"
      ]
    },
    {
      "page": "vis.immunr_dynamics",
      "title": "Visualise clonotype dynamics",
      "concept": [
        "dynamics"
      ],
      "topics": [
        "vis.immunr_dynamics"
      ]
    },
    {
      "page": "vis.immunr_exp_vol",
      "title": "Visualise results of the exploratory analysis",
      "concept": [
        "explore"
      ],
      "topics": [
        "vis.immunr_exp_clones",
        "vis.immunr_exp_count",
        "vis.immunr_exp_len",
        "vis.immunr_exp_vol"
      ]
    },
    {
      "page": "vis.immunr_gene_usage",
      "title": "Histograms and boxplots (general case / gene usage)",
      "concept": [
        "gene_usage"
      ],
      "topics": [
        "vis.immunr_gene_usage"
      ]
    },
    {
      "page": "vis.immunr_hclust",
      "title": "Visualisation of hierarchical clustering",
      "concept": [
        "post_analysis"
      ],
      "topics": [
        "vis.immunr_hclust"
      ]
    },
    {
      "page": "vis.immunr_inc_overlap",
      "title": "Visualise incremental overlaps",
      "concept": [
        "overlap"
      ],
      "topics": [
        "vis.immunr_inc_overlap"
      ]
    },
    {
      "page": "vis.immunr_kmeans",
      "title": "Visualisation of K-means and DBSCAN clustering",
      "concept": [
        "post_analysis"
      ],
      "topics": [
        "vis.immunr_dbscan",
        "vis.immunr_kmeans"
      ]
    },
    {
      "page": "vis.immunr_kmer_table",
      "title": "Most frequent kmers visualisation.",
      "concept": [
        "kmers"
      ],
      "topics": [
        "vis.immunr_kmer_table"
      ]
    },
    {
      "page": "vis.immunr_mds",
      "title": "PCA / MDS / tSNE visualisation (mainly overlap / gene usage)",
      "concept": [
        "post_analysis"
      ],
      "topics": [
        "vis.immunr_mds",
        "vis.immunr_pca",
        "vis.immunr_tsne"
      ]
    },
    {
      "page": "vis.immunr_ov_matrix",
      "title": "Repertoire overlap and gene usage visualisations",
      "concept": [
        "overlap"
      ],
      "topics": [
        "vis.immunr_gu_matrix",
        "vis.immunr_ov_matrix"
      ]
    },
    {
      "page": "vis.immunr_public_repertoire",
      "title": "Public repertoire visualisation",
      "concept": [
        "pubrep"
      ],
      "topics": [
        "vis.immunr_public_repertoire"
      ]
    },
    {
      "page": "vis.immunr_public_statistics",
      "title": "Visualise sharing of clonotypes among samples",
      "concept": [
        "pubrep"
      ],
      "topics": [
        "vis.immunr_public_statistics"
      ]
    },
    {
      "page": "vis.step_failure_ignored",
      "title": "Handler for .nofail argument of pipeline steps that prevents examples from crashing on computers where certain dependencies are not installed",
      "topics": [
        "vis.step_failure_ignored"
      ]
    }
  ],
  "_readme": "https://github.com/immunomind/immunarch/raw/HEAD/README.md",
  "_rundeps": [
    "airr",
    "ape",
    "backports",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "checkmate",
    "circlize",
    "cli",
    "clipr",
    "codetools",
    "collections",
    "colorspace",
    "cpp11",
    "crayon",
    "data.table",
    "DBI",
    "dbplyr",
    "digest",
    "doParallel",
    "dplyr",
    "dtplyr",
    "duckdb",
    "duckplyr",
    "farver",
    "fastmap",
    "foreach",
    "generics",
    "ggplot2",
    "ggsci",
    "ggthemes",
    "GlobalOptions",
    "glue",
    "gtable",
    "hms",
    "immundata",
    "isoband",
    "iterators",
    "jsonlite",
    "labeling",
    "lattice",
    "lifecycle",
    "magrittr",
    "memoise",
    "nlme",
    "patchwork",
    "pheatmap",
    "pillar",
    "pkgconfig",
    "plyr",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "readr",
    "reshape2",
    "rlang",
    "rlist",
    "S7",
    "scales",
    "shape",
    "stringdist",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "tzdb",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr",
    "XML",
    "yaml"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "immunarch.Rmd",
      "filename": "immunarch.html",
      "title": "Immunarch overview",
      "engine": "knitr::rmarkdown",
      "headings": [
        "🧬 immunarch – Multi-modal immune repertoire analysis in R",
        "🤔 Why immunarch?",
        "📦 Installation",
        "Prerequisites",
        "Install the latest version",
        "Other installation options",
        "⚡ Quick Start",
        "📄 Documentation",
        "🪲 Bugs and Issues",
        "🏷 About",
        "Citation",
        "License",
        "Author and contributors",
        "Commercial usage"
      ],
      "created": "2025-10-10 09:10:59",
      "modified": "2025-10-14 15:10:03",
      "commits": 2
    },
    {
      "source": "immunarch_threads.Rmd",
      "filename": "immunarch_threads.html",
      "title": "Limit the number of threads used by immunarch",
      "engine": "knitr::rmarkdown",
      "headings": [
        "What is happening under the hood?",
        "Why limit threads?",
        "How to limit the number of threads",
        "References"
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