{
  "_id": "6a15b793acfb0bcc41d67810",
  "Package": "shazam",
  "Type": "Package",
  "Version": "1.3.2.999",
  "Date": "2026-05-26",
  "Authors@R": "c(person(\"Mohamed\", \"Uduman\", role=c(\"aut\"), \nemail=\"mohamed.uduman@yale.edu\"),\nperson(\"Namita\", \"Gupta\", role=c(\"aut\"),\nemail=\"namita.gupta@yale.edu\"),\nperson(\"Susanna\", \"Marquez\", role=c(\"aut\",\"cre\"),\nemail=\"susanna.marquez@yale.edu\"),\nperson(\"Julian\", \"Zhou\", role=c(\"aut\"),\nemail=\"julian.zhou@yale.edu\"),\nperson(\"Nima\", \"Nouri\", role=c(\"aut\"),\nemail=\"nima.nouri@yale.edu\"),\nperson(\"Noah\", \"Yann Lee\", role=c(\"aut\"),\nemail=\"noah.yann.lee@yale.edu\"),\nperson(\"Ang\", \"Cui\", role=c(\"ctb\"),\nemail=\"angcui@mit.edu\"),\nperson(\"Jason\", \"Vander Heiden\", role=c(\"aut\"),\nemail=\"jason.vanderheiden@gmail.com\"),\nperson(\"Gur\", \"Yaari\", role=c(\"aut\"),\nemail=\"gur.yaari@biu.ac.il\"),\nperson(\"Steven\", \"Kleinstein\", role=c(\"aut\", \"cph\"),\nemail=\"steven.kleinstein@yale.edu\"))",
  "Title": "Immunoglobulin Somatic Hypermutation Analysis",
  "Description": "Provides a computational framework for analyzing mutations\nin immunoglobulin (Ig) sequences. Includes methods for Bayesian\nestimation of antigen-driven selection pressure, mutational\nload quantification, building of somatic hypermutation (SHM)\nmodels, and model-dependent distance calculations. Also\nincludes empirically derived models of SHM for both mice and\nhumans. Citations: Gupta and Vander Heiden, et al (2015)\n<doi:10.1093/bioinformatics/btv359>, Yaari, et al (2012)\n<doi:10.1093/nar/gks457>, Yaari, et al (2013)\n<doi:10.3389/fimmu.2013.00358>, Cui, et al (2016)\n<doi:10.4049/jimmunol.1502263>.",
  "License": "AGPL-3",
  "URL": "http://shazam.readthedocs.io",
  "BugReports": "https://github.com/immcantation/shazam/issues",
  "LazyData": "true",
  "BuildVignettes": "true",
  "VignetteBuilder": "knitr, rmarkdown",
  "Encoding": "UTF-8",
  "biocViews": "",
  "Collate": "'Shazam.R' 'Core.R' 'RegionDefinitions.R' 'Baseline.R'\n'ConvertNumbering.R' 'MutationProfiling.R' 'Deprecated.R'\n'DistToNearest.R' 'MutationDefinitions.R' 'RegionsExtend.R'\n'Shmulate.R' 'TargetingModels.R' 'kedd.R'",
  "RoxygenNote": "7.3.3",
  "Config/pak/sysreqs": "libglpk-dev libbz2-dev libicu-dev liblzma-dev\nlibxml2-dev libx11-dev xz-utils zlib1g-dev",
  "Repository": "https://immcantation.r-universe.dev",
  "Date/Publication": "2026-05-26 08:50:38 UTC",
  "RemoteUrl": "https://github.com/immcantation/shazam",
  "RemoteRef": "HEAD",
  "RemoteSha": "cdf9f1c6712c1437cc9b13171fccd395de84d8df",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-26 15:02:50 UTC",
    "User": "root"
  },
  "Author": "Mohamed Uduman [aut],\nNamita Gupta [aut],\nSusanna Marquez [aut, cre],\nJulian Zhou [aut],\nNima Nouri [aut],\nNoah Yann Lee [aut],\nAng Cui [ctb],\nJason Vander Heiden [aut],\nGur Yaari [aut],\nSteven Kleinstein [aut, cph]",
  "Maintainer": "Susanna Marquez <susanna.marquez@yale.edu>",
  "MD5sum": "57a621127743de6e8aaad612c19a9faa",
  "_user": "immcantation",
  "_type": "src",
  "_file": "shazam_1.3.2.999.tar.gz",
  "_fileid": "0c0d23aab89aab9d7cf597b3d0ee3897a623f6cd7f04d559cc2b4f0ab27cee1b",
  "_filesize": 1895898,
  "_sha256": "0c0d23aab89aab9d7cf597b3d0ee3897a623f6cd7f04d559cc2b4f0ab27cee1b",
  "_created": "2026-05-26T15:02:50.000Z",
  "_published": "2026-05-26T15:09:07.212Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77892116191,
      "time": 308,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7218358034"
    },
    {
      "job": 77892116058,
      "time": 312,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7218359696"
    },
    {
      "job": 77892115979,
      "time": 215,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7218349598"
    },
    {
      "job": 77892116065,
      "time": 175,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7218352736"
    },
    {
      "job": 77890838036,
      "time": 339,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7218222694"
    },
    {
      "job": 77892115941,
      "time": 151,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7218287534"
    },
    {
      "job": 77892116083,
      "time": 292,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7218353190"
    },
    {
      "job": 77892115931,
      "time": 282,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7218346710"
    },
    {
      "job": 77892115948,
      "time": 240,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7218327929"
    }
  ],
  "_buildurl": "https://github.com/r-universe/immcantation/actions/runs/26456196718",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/immcantation/shazam",
  "_commit": {
    "id": "cdf9f1c6712c1437cc9b13171fccd395de84d8df",
    "author": "github-actions[bot] <github-actions[bot]@users.noreply.github.com>",
    "committer": "github-actions[bot] <github-actions[bot]@users.noreply.github.com>",
    "message": "[skip ci] Auto-render docs.\n",
    "time": 1779785438
  },
  "_maintainer": {
    "name": "Susanna Marquez",
    "email": "susanna.marquez@yale.edu",
    "login": "ssnn-airr",
    "description": "",
    "uuid": 20683719
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "ggplot2",
      "version": ">= 3.4.0",
      "role": "Depends"
    },
    {
      "package": "alakazam",
      "version": ">= 1.4.1",
      "role": "Imports"
    },
    {
      "package": "ape",
      "role": "Imports"
    },
    {
      "package": "diptest",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "version": ">= 1.0",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "version": ">= 1.5.0",
      "role": "Imports"
    },
    {
      "package": "iterators",
      "role": "Imports"
    },
    {
      "package": "KernSmooth",
      "role": "Imports"
    },
    {
      "package": "lazyeval",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "progress",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "seqinr",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "stringi",
      "version": ">= 1.1.3",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "tidyselect",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "tibble",
      "role": "Suggests"
    }
  ],
  "_owner": "immcantation",
  "_selfowned": true,
  "_usedby": 2,
  "_updates": [
    {
      "week": "2025-25",
      "n": 1
    },
    {
      "week": "2025-29",
      "n": 3
    },
    {
      "week": "2025-30",
      "n": 8
    },
    {
      "week": "2025-31",
      "n": 1
    },
    {
      "week": "2025-37",
      "n": 1
    },
    {
      "week": "2026-16",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 18
    },
    {
      "week": "2026-22",
      "n": 2
    }
  ],
  "_tags": [
    {
      "name": "1.3.0",
      "date": "2025-10-20"
    },
    {
      "name": "1.3.1",
      "date": "2025-12-26"
    },
    {
      "name": "1.3.2",
      "date": "2026-04-30"
    }
  ],
  "_stars": 2,
  "_contributors": [
    {
      "user": "ssnn-airr",
      "count": 517,
      "uuid": 20683719
    },
    {
      "user": "javh",
      "count": 387,
      "uuid": 4105629
    },
    {
      "user": "julianqz",
      "count": 205,
      "uuid": 7434521
    },
    {
      "user": "namita1025",
      "count": 67,
      "uuid": 6172391
    },
    {
      "user": "mohameduduman",
      "count": 64,
      "uuid": 8083920
    },
    {
      "user": "angcui",
      "count": 21,
      "uuid": 83384433
    },
    {
      "user": "eba28",
      "count": 14,
      "uuid": 43794704
    },
    {
      "user": "muduman",
      "count": 9,
      "uuid": 7604483
    },
    {
      "user": "ggabernet",
      "count": 7,
      "uuid": 3973503
    },
    {
      "user": "burhansabuwala",
      "count": 6,
      "uuid": 52125885
    },
    {
      "user": "noahyannlee",
      "count": 4,
      "uuid": 71304278
    },
    {
      "user": "copilot",
      "count": 4,
      "uuid": 198982749
    },
    {
      "user": "kbhoehn",
      "count": 3,
      "uuid": 20629514
    },
    {
      "user": "milcat",
      "count": 2,
      "uuid": 35433127
    },
    {
      "user": "purpleavatar",
      "count": 1,
      "uuid": 22361216
    }
  ],
  "_userbio": {
    "uuid": 52156905,
    "type": "organization",
    "name": "Immcantation"
  },
  "_downloads": {
    "count": 1370,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/shazam"
  },
  "_devurl": "https://github.com/immcantation/shazam",
  "_searchresults": 348,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/shazam.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/immcantation/shazam",
  "_realowner": "immcantation",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.2",
      "date": "2016-02-21"
    },
    {
      "version": "0.1.3",
      "date": "2016-07-31"
    },
    {
      "version": "0.1.4",
      "date": "2016-08-05"
    },
    {
      "version": "0.1.5",
      "date": "2017-03-24"
    },
    {
      "version": "0.1.6",
      "date": "2017-05-12"
    },
    {
      "version": "0.1.7",
      "date": "2017-05-14"
    },
    {
      "version": "0.1.8",
      "date": "2017-06-30"
    },
    {
      "version": "0.1.9",
      "date": "2018-03-31"
    },
    {
      "version": "0.1.10",
      "date": "2018-09-20"
    },
    {
      "version": "0.1.11",
      "date": "2019-01-28"
    },
    {
      "version": "0.2.0",
      "date": "2019-07-19"
    },
    {
      "version": "0.2.1",
      "date": "2019-07-20"
    },
    {
      "version": "0.2.2",
      "date": "2019-12-16"
    },
    {
      "version": "0.2.3",
      "date": "2020-02-06"
    },
    {
      "version": "1.0.0",
      "date": "2020-05-11"
    },
    {
      "version": "1.0.1",
      "date": "2020-07-19"
    },
    {
      "version": "1.0.2",
      "date": "2020-08-11"
    },
    {
      "version": "1.1.0",
      "date": "2021-07-08"
    },
    {
      "version": "1.1.1",
      "date": "2022-05-24"
    },
    {
      "version": "1.1.2",
      "date": "2022-10-01"
    },
    {
      "version": "1.2.0",
      "date": "2023-10-02"
    },
    {
      "version": "1.3.0",
      "date": "2025-10-20"
    },
    {
      "version": "1.3.1",
      "date": "2026-01-08"
    },
    {
      "version": "1.3.2",
      "date": "2026-05-01"
    }
  ],
  "_exports": [
    "as.data.frame",
    "calcBaseline",
    "calcExpectedMutations",
    "calcObservedMutations",
    "calcTargetingDistance",
    "calculateMutability",
    "collapseClones",
    "consensusSequence",
    "convertNumbering",
    "createBaseline",
    "createMutabilityMatrix",
    "createMutationDefinition",
    "createRegionDefinition",
    "createSubstitutionMatrix",
    "createTargetingMatrix",
    "createTargetingModel",
    "distToNearest",
    "editBaseline",
    "expectedMutations",
    "extendMutabilityMatrix",
    "extendSubstitutionMatrix",
    "findThreshold",
    "groupBaseline",
    "makeAverage1merMut",
    "makeAverage1merSub",
    "makeDegenerate5merMut",
    "makeDegenerate5merSub",
    "makeGraphDf",
    "minNumMutationsTune",
    "minNumSeqMutationsTune",
    "observedMutations",
    "plot",
    "plotBaselineDensity",
    "plotBaselineSummary",
    "plotDensityThreshold",
    "plotGmmThreshold",
    "plotMutability",
    "plotSlideWindowTune",
    "plotTune",
    "print",
    "setRegionBoundaries",
    "shmulateSeq",
    "shmulateTree",
    "slideWindowDb",
    "slideWindowSeq",
    "slideWindowTune",
    "slideWindowTunePlot",
    "summarizeBaseline",
    "summary",
    "testBaseline",
    "writeTargetingDistance"
  ],
  "_datasets": [
    {
      "name": "CHARGE_MUTATIONS",
      "title": "",
      "object": "CHARGE_MUTATIONS",
      "class": [
        "MutationDefinition"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "HH_S1F",
      "title": "",
      "object": "HH_S1F",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "A",
        "C",
        "G",
        "T"
      ],
      "rows": 4,
      "table": true,
      "tojson": true
    },
    {
      "name": "HH_S5F",
      "title": "",
      "object": "HH_S5F",
      "class": [
        "TargetingModel"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "HKL_S1F",
      "title": "",
      "object": "HKL_S1F",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "A",
        "C",
        "G",
        "T"
      ],
      "rows": 4,
      "table": true,
      "tojson": true
    },
    {
      "name": "HKL_S5F",
      "title": "",
      "object": "HKL_S5F",
      "class": [
        "TargetingModel"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "HYDROPATHY_MUTATIONS",
      "title": "",
      "object": "HYDROPATHY_MUTATIONS",
      "class": [
        "MutationDefinition"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "IMGT_V",
      "title": "",
      "object": "IMGT_V",
      "class": [
        "RegionDefinition"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "IMGT_V_BY_CODONS",
      "title": "",
      "object": "IMGT_V_BY_CODONS",
      "class": [
        "RegionDefinition"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "IMGT_V_BY_REGIONS",
      "title": "",
      "object": "IMGT_V_BY_REGIONS",
      "class": [
        "RegionDefinition"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "IMGT_V_BY_SEGMENTS",
      "title": "",
      "object": "IMGT_V_BY_SEGMENTS",
      "class": [
        "RegionDefinition"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "IMGT_VDJ",
      "title": "",
      "object": "IMGT_VDJ",
      "class": [
        "RegionDefinition"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "IMGT_VDJ_BY_REGIONS",
      "title": "",
      "object": "IMGT_VDJ_BY_REGIONS",
      "class": [
        "RegionDefinition"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "MK_RS1NF",
      "title": "",
      "object": "MK_RS1NF",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "A",
        "C",
        "G",
        "T"
      ],
      "rows": 4,
      "table": true,
      "tojson": true
    },
    {
      "name": "MK_RS5NF",
      "title": "",
      "object": "MK_RS5NF",
      "class": [
        "TargetingModel"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "POLARITY_MUTATIONS",
      "title": "",
      "object": "POLARITY_MUTATIONS",
      "class": [
        "MutationDefinition"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "U5N",
      "title": "",
      "object": "U5N",
      "class": [
        "TargetingModel"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "VOLUME_MUTATIONS",
      "title": "",
      "object": "VOLUME_MUTATIONS",
      "class": [
        "MutationDefinition"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [],
  "_readme": "https://github.com/immcantation/shazam/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "ade4",
    "airr",
    "alakazam",
    "ape",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "cigarillo",
    "cli",
    "clipr",
    "codetools",
    "cpp11",
    "crayon",
    "DelayedArray",
    "digest",
    "diptest",
    "doParallel",
    "dplyr",
    "farver",
    "foreach",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "hms",
    "igraph",
    "IRanges",
    "isoband",
    "iterators",
    "jsonlite",
    "KernSmooth",
    "labeling",
    "lambda.r",
    "lattice",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "nlme",
    "pillar",
    "pixmap",
    "pkgconfig",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "readr",
    "Rhtslib",
    "rlang",
    "Rsamtools",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "segmented",
    "Seqinfo",
    "seqinr",
    "snow",
    "sp",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "tibble",
    "tidyr",
    "tidyselect",
    "tzdb",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "DistToNearest-Vignette.Rmd",
      "filename": "DistToNearest-Vignette.html",
      "title": "Shazam: Tuning clonal assignment thresholds with nearest neighbor distances",
      "author": "Namita Gupta, Susanna Marquez, Nima Nouri and Julian Q. Zhou",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Example data",
        "Calculating nearest neighbor distances (heavy chain sequences)",
        "Calculating nearest neighbor distances (single-cell paired heavy and light chain sequences)",
        "Using nearest neighbor distances to determine clonal assignment thresholds",
        "Threshold determination by manual inspection",
        "Automated threshold detection via smoothed density",
        "Automated threshold detection via a mixture model",
        "Calculating nearest neighbor distances independently for subsets of data",
        "Calculating nearest neighbor distances across groups rather than within a groups",
        "Speeding up pairwise-distance-matrix calculations with subsampling"
      ],
      "created": "2015-02-04 21:12:39",
      "modified": "2024-04-02 19:34:07",
      "commits": 68
    },
    {
      "source": "Mutation-Vignette.Rmd",
      "filename": "Mutation-Vignette.html",
      "title": "Shazam: Mutation analysis",
      "author": "Susanna Marquez & Julian Q. Zhou",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Example data",
        "Calculate the counts and frequencies of mutations over the entire sequence",
        "Calculate mutations within subregions",
        "Use amino acid physicochemical properties to define mutations"
      ],
      "created": "2017-04-03 19:53:02",
      "modified": "2023-11-06 13:25:57",
      "commits": 17
    },
    {
      "source": "Baseline-Vignette.Rmd",
      "filename": "Baseline-Vignette.html",
      "title": "Shazam: Quantification of selection pressure",
      "author": "Namita Gupta & Jason Anthony Vander Heiden & Julian Q. Zhou",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Example data",
        "Preprocessing",
        "Constructing clonal consensus sequences",
        "Incorporating lineage information",
        "Calculate selection PDFs for individual sequences",
        "Calculating selection in multiple steps",
        "Calculating selection in one step",
        "Using alternative mutation definitions and models",
        "Group and convolve individual selection distributions",
        "Grouping by a single annotation",
        "Subsetting and grouping by multiple annotations",
        "Convolving variables at multiple levels",
        "Testing the difference in selection PDFs between groups",
        "Plot and compare selection scores for groups",
        "Editing a field in a Baseline object"
      ],
      "created": "2015-04-28 18:34:40",
      "modified": "2024-04-02 19:34:07",
      "commits": 57
    },
    {
      "source": "Targeting-Vignette.Rmd",
      "filename": "Targeting-Vignette.html",
      "title": "Shazam: Inferring SHM targeting models",
      "author": "Namita Gupta & Julian Q. Zhou",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Example data",
        "Infer targeting model (substitution and mutability)",
        "Visualize targeting model",
        "Calculate targeting distance matrix"
      ],
      "created": "2015-04-25 19:27:21",
      "modified": "2024-04-02 19:34:07",
      "commits": 40
    },
    {
      "source": "Shmulate-Vignette.Rmd",
      "filename": "Shmulate-Vignette.html",
      "title": "Shazam: Simulating sequence mutations",
      "author": "Julian Q. Zhou",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Simulate mutations in a single sequence",
        "Simulate mutations in a lineage tree"
      ],
      "created": "2018-03-16 14:35:11",
      "modified": "2026-04-30 11:20:09",
      "commits": 12
    }
  ],
  "_score": 9.204639088492833,
  "_indexed": true,
  "_nocasepkg": "shazam",
  "_universes": [
    "immcantation",
    "ssnn-airr"
  ],
  "_previous": "1.3.2",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.3.2.999",
      "date": "2026-05-26T15:06:05.000Z",
      "distro": "noble",
      "commit": "cdf9f1c6712c1437cc9b13171fccd395de84d8df",
      "fileid": "c82c624e8baa42d8c64adde2d91417b8b6f96044ee3000a9a8d8e56dd879370d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/immcantation/actions/runs/26456196718"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.3.2.999",
      "date": "2026-05-26T15:06:14.000Z",
      "distro": "noble",
      "commit": "cdf9f1c6712c1437cc9b13171fccd395de84d8df",
      "fileid": "45f60ecd1e3b7eabdca379e0d642a1be2688364a8877a5aa2d6df854bc98f65c",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/immcantation/actions/runs/26456196718"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.3.2.999",
      "date": "2026-05-26T15:06:34.000Z",
      "commit": "cdf9f1c6712c1437cc9b13171fccd395de84d8df",
      "fileid": "e70ec733ee52b13f061bce36148e00e82b51f7b136b4189adf162ee2deaa2b06",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/immcantation/actions/runs/26456196718"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.3.2.999",
      "date": "2026-05-26T15:06:56.000Z",
      "commit": "cdf9f1c6712c1437cc9b13171fccd395de84d8df",
      "fileid": "7cc5824791ccc4f93e8603965b7f970eb05ae16929ea8edbb996fbdf980df1d6",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/immcantation/actions/runs/26456196718"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.3.2.999",
      "date": "2026-05-26T15:06:02.000Z",
      "commit": "cdf9f1c6712c1437cc9b13171fccd395de84d8df",
      "fileid": "2a4d60dd3e1d1e3d0bab44b45bf18c9b21de10d6c64768ffd80cedf1902b68ca",
      "status": "success",
      "buildurl": "https://github.com/r-universe/immcantation/actions/runs/26456196718"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.3.2.999",
      "date": "2026-05-26T15:05:40.000Z",
      "commit": "cdf9f1c6712c1437cc9b13171fccd395de84d8df",
      "fileid": "d14c249608cdaf40f9b833749830b52ba7d2ce5d837072dae7b575b96f189022",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/immcantation/actions/runs/26456196718"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.3.2.999",
      "date": "2026-05-26T15:05:16.000Z",
      "commit": "cdf9f1c6712c1437cc9b13171fccd395de84d8df",
      "fileid": "76bfe1b833872f48f045f337657eb61ffe415b4408a24b7b1d57fc1855835b02",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/immcantation/actions/runs/26456196718"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.3.2.999",
      "date": "2026-05-26T15:04:55.000Z",
      "commit": "cdf9f1c6712c1437cc9b13171fccd395de84d8df",
      "fileid": "9e69478bf67fc8790e250840d19f356309f4322118ad08c98c8bea79c77903ae",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/immcantation/actions/runs/26456196718"
    }
  ]
}