{
  "_id": "6a1af6ba1d7bb097a09f9e4c",
  "Package": "musicatk",
  "Type": "Package",
  "Title": "Mutational Signature Comprehensive Analysis Toolkit",
  "Version": "2.7.0",
  "Authors@R": "c(person(\"Aaron\", \"Chevalier\", email = \"atgc@bu.edu\", role = \"aut\", comment = c(ORCHID = \"0000-0002-3968-9250\")), person(\"Natasha\", \"Gurevich\", email = \"nqg@bu.edu\", role = \"aut\", comment = c(ORCHID = \"0000-0002-0747-6840\")), person(\"Tao\", \"Guo\", email = \"guo1241@gmail.com\", role = \"aut\", comment = c(ORCHID = \"0009-0005-8960-9203\")), person(given=c(\"Joshua\",\"D.\"), family=\"Campbell\", email=\"camp@bu.edu\", role=c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-0780-8662\")))",
  "Description": "Mutational signatures are carcinogenic exposures or\naberrant cellular processes that can cause alterations to the\ngenome. We created musicatk (MUtational SIgnature Comprehensive\nAnalysis ToolKit) to address shortcomings in versatility and\nease of use in other pre-existing computational tools. Although\nmany different types of mutational data have been generated,\ncurrent software packages do not have a flexible framework to\nallow users to mix and match different types of mutations in\nthe mutational signature inference process. Musicatk enables\nusers to count and combine multiple mutation types, including\nSBS, DBS, and indels. Musicatk calculates replication strand,\ntranscription strand and combinations of these features along\nwith discovery from unique and proprietary genomic feature\nassociated with any mutation type. Musicatk also implements\nseveral methods for discovery of new signatures as well as\nmethods to infer exposure given an existing set of signatures.\nMusicatk provides functions for visualization and downstream\nexploratory analysis including the ability to compare\nsignatures between cohorts and find matching signatures in\nCOSMIC V2 or COSMIC V3.",
  "License": "LGPL-3",
  "URL": "https://www.camplab.net/musicatk/",
  "BugReports": "https://github.com/campbio/musicatk/issues",
  "Encoding": "UTF-8",
  "LazyData": "TRUE",
  "biocViews": "Software, BiologicalQuestion, SomaticMutation,\nVariantAnnotation",
  "RoxygenNote": "7.3.2",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibfribidi-dev make libgsl0-dev libharfbuzz-dev libbz2-dev\nlibicu-dev libjpeg-dev liblzma-dev libpng-dev libtiff-dev\nlibuv1-dev libwebp-dev libxml2-dev libssl-dev perl libx11-dev\nxz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:54:13 UTC",
  "RemoteUrl": "https://github.com/bioc/musicatk",
  "RemoteRef": "HEAD",
  "RemoteSha": "4eabe7f8aecc2a4490cd6b60178b9db348a92d5c",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:44:36 UTC",
    "User": "root"
  },
  "Author": "Aaron Chevalier [aut] (ORCHID: 0000-0002-3968-9250),\nNatasha Gurevich [aut] (ORCHID: 0000-0002-0747-6840),\nTao Guo [aut] (ORCHID: 0009-0005-8960-9203),\nJoshua D. Campbell [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-0780-8662>)",
  "Maintainer": "Joshua D. Campbell <camp@bu.edu>",
  "MD5sum": "58d7db811c6a8cf61de5dca5e3389169",
  "_user": "bioc",
  "_type": "src",
  "_file": "musicatk_2.7.0.tar.gz",
  "_fileid": "1c211edcad88f509be8d669382686e105562bcae41a5627df3690eb7d468d1d5",
  "_filesize": 6111330,
  "_sha256": "1c211edcad88f509be8d669382686e105562bcae41a5627df3690eb7d468d1d5",
  "_created": "2026-05-30T09:44:36.000Z",
  "_published": "2026-05-30T14:39:54.831Z",
  "_jobs": [
    {
      "job": 78640530855,
      "time": 477,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307484103"
    },
    {
      "job": 78640530865,
      "time": 1089,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307534682"
    },
    {
      "job": 78640530862,
      "time": 1097,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307535443"
    },
    {
      "job": 78640530857,
      "time": 986,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7308938610"
    },
    {
      "job": 78640530854,
      "time": 550,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7308890422"
    },
    {
      "job": 78639462802,
      "time": 754,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307278810"
    },
    {
      "job": 78640530856,
      "time": 478,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 78640530879,
      "time": 809,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307510337"
    },
    {
      "job": 78640530882,
      "time": 840,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307511540"
    },
    {
      "job": 78640530884,
      "time": 751,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307505237"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 16
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26675586046",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/musicatk",
  "_commit": {
    "id": "4eabe7f8aecc2a4490cd6b60178b9db348a92d5c",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380853
  },
  "_maintainer": {
    "name": "Joshua D. Campbell",
    "email": "camp@bu.edu",
    "login": "camplab",
    "description": "",
    "uuid": 43044384,
    "orcid": "0000-0003-0780-8662"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.4.0",
      "role": "Depends"
    },
    {
      "package": "NMF",
      "role": "Depends"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "VariantAnnotation",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "role": "Imports"
    },
    {
      "package": "base",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "gtools",
      "role": "Imports"
    },
    {
      "package": "gridExtra",
      "role": "Imports"
    },
    {
      "package": "MCMCprecision",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "matrixTests",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "BSgenome",
      "role": "Imports"
    },
    {
      "package": "GenomeInfoDb",
      "role": "Imports"
    },
    {
      "package": "GenomicFeatures",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "uwot",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "TxDb.Hsapiens.UCSC.hg19.knownGene",
      "role": "Imports"
    },
    {
      "package": "TxDb.Hsapiens.UCSC.hg38.knownGene",
      "role": "Imports"
    },
    {
      "package": "BSgenome.Hsapiens.UCSC.hg19",
      "role": "Imports"
    },
    {
      "package": "BSgenome.Hsapiens.UCSC.hg38",
      "role": "Imports"
    },
    {
      "package": "BSgenome.Mmusculus.UCSC.mm9",
      "role": "Imports"
    },
    {
      "package": "BSgenome.Mmusculus.UCSC.mm10",
      "role": "Imports"
    },
    {
      "package": "decompTumor2Sig",
      "role": "Imports"
    },
    {
      "package": "topicmodels",
      "role": "Imports"
    },
    {
      "package": "ggrepel",
      "role": "Imports"
    },
    {
      "package": "plotly",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "factoextra",
      "role": "Imports"
    },
    {
      "package": "cluster",
      "role": "Imports"
    },
    {
      "package": "ComplexHeatmap",
      "role": "Imports"
    },
    {
      "package": "philentropy",
      "role": "Imports"
    },
    {
      "package": "maftools",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "role": "Imports"
    },
    {
      "package": "stringi",
      "role": "Imports"
    },
    {
      "package": "tidyverse",
      "role": "Imports"
    },
    {
      "package": "ggpubr",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "version": ">= 1.6.1",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "TCGAbiolinks",
      "role": "Suggests"
    },
    {
      "package": "shinyBS",
      "role": "Suggests"
    },
    {
      "package": "shinyalert",
      "role": "Suggests"
    },
    {
      "package": "shinybusy",
      "role": "Suggests"
    },
    {
      "package": "shinydashboard",
      "role": "Suggests"
    },
    {
      "package": "shinyjs",
      "role": "Suggests"
    },
    {
      "package": "shinyjqui",
      "role": "Suggests"
    },
    {
      "package": "sortable",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "survival",
      "role": "Suggests"
    },
    {
      "package": "XVector",
      "role": "Suggests"
    },
    {
      "package": "qpdf",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "shinyWidgets",
      "role": "Suggests"
    },
    {
      "package": "cowplot",
      "role": "Suggests"
    },
    {
      "package": "withr",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-29",
      "n": 3
    },
    {
      "week": "2025-30",
      "n": 2
    },
    {
      "week": "2025-41",
      "n": 2
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.7.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "2.6.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "biologicalquestion",
    "somaticmutation",
    "variantannotation"
  ],
  "_stars": 16,
  "_contributors": [
    {
      "user": "joshua-d-campbell",
      "count": 48,
      "uuid": 14353256
    },
    {
      "user": "achevali",
      "count": 36,
      "uuid": 6088871
    },
    {
      "user": "jwokaty",
      "count": 11,
      "uuid": 1744257
    },
    {
      "user": "nqgurevich",
      "count": 10,
      "uuid": 84352235
    },
    {
      "user": "nturaga",
      "count": 8,
      "uuid": 2746443
    },
    {
      "user": "gtnick1241",
      "count": 7,
      "uuid": 111305657
    },
    {
      "user": "nathansahelijo",
      "count": 5,
      "uuid": 22963977
    },
    {
      "user": "biotong",
      "count": 2,
      "uuid": 22845553
    },
    {
      "user": "zeenu94",
      "count": 1,
      "uuid": 56841101
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 369,
    "source": "https://www.bioconductor.org/packages/stats/bioc/musicatk"
  },
  "_devurl": "https://github.com/campbio/musicatk",
  "_searchresults": 15,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/musicatk.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/campbio/musicatk",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "%>%",
    "add_flank_to_variants",
    "add_result",
    "annotate_replication_strand",
    "annotate_transcript_strand",
    "annotate_variant_length",
    "annotate_variant_type",
    "auto_predict_grid",
    "build_custom_table",
    "build_standard_table",
    "built_tables",
    "cluster_exposure",
    "combine_count_tables",
    "combine_predict_grid",
    "compare_cosmic_v2",
    "compare_cosmic_v3",
    "compare_k_vals",
    "compare_results",
    "cosmic_v2_subtype_map",
    "create_musica_from_counts",
    "create_musica_from_variants",
    "create_umap",
    "credible_intervals",
    "credible_intervals<-",
    "discover_signatures",
    "drop_annotation",
    "exposure_differential_analysis",
    "exposures",
    "exposures<-",
    "extract_count_tables",
    "extract_variants",
    "extract_variants_from_maf",
    "extract_variants_from_maf_file",
    "extract_variants_from_matrix",
    "extract_variants_from_vcf",
    "extract_variants_from_vcf_file",
    "generate_result_grid",
    "get_count_table",
    "get_modality",
    "get_model",
    "get_result_list_entry",
    "hyperparameter",
    "hyperparameter<-",
    "k_select",
    "metrics",
    "metrics<-",
    "modality",
    "modality<-",
    "model_id",
    "model_id<-",
    "musicatk",
    "name_signatures",
    "num_signatures",
    "num_signatures<-",
    "other_parameters",
    "other_parameters<-",
    "parameter",
    "parameter<-",
    "plot_cluster",
    "plot_differential_analysis",
    "plot_exposures",
    "plot_heatmap",
    "plot_k_comparison",
    "plot_sample_counts",
    "plot_sample_reconstruction_error",
    "plot_signatures",
    "plot_umap",
    "predict_exposure",
    "rc",
    "result_list",
    "result_list<-",
    "samp_annot",
    "samp_annot<-",
    "sample_names",
    "select_genome",
    "signatures",
    "signatures<-",
    "subset_musica_by_annotation",
    "subset_musica_by_counts",
    "subset_variant_by_type",
    "subset_variants_by_samples",
    "table_selected",
    "tables",
    "tables<-",
    "umap",
    "umap<-",
    "variants",
    "variants<-"
  ],
  "_datasets": [
    {
      "name": "cosmic_v2_sigs",
      "title": "COSMIC v2 SBS96 Signatures Result Object",
      "object": "cosmic_v2_sigs",
      "class": [
        "result_model"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "cosmic_v3_dbs_sigs",
      "title": "COSMIC v3 DBS Genome Signatures Result Object",
      "object": "cosmic_v3_dbs_sigs",
      "class": [
        "result_model"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "cosmic_v3_indel_sigs",
      "title": "COSMIC v3 Indel Genome Signatures Result Object",
      "object": "cosmic_v3_indel_sigs",
      "class": [
        "result_model"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "cosmic_v3_sbs_sigs",
      "title": "COSMIC v3 SBS96 Genome Signatures Result Object",
      "object": "cosmic_v3_sbs_sigs",
      "class": [
        "result_model"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "cosmic_v3_sbs_sigs_exome",
      "title": "COSMIC v3 SBS96 Exome Signatures Result Object",
      "object": "cosmic_v3_sbs_sigs_exome",
      "class": [
        "result_model"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "dbs_musica",
      "title": "dbs_musica",
      "object": "dbs_musica",
      "class": [
        "musica"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "indel_musica",
      "title": "indel_musica",
      "object": "indel_musica",
      "class": [
        "musica"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "musica",
      "title": "musica",
      "object": "musica",
      "class": [
        "musica"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "musica_annot",
      "title": "musica_annot",
      "object": "musica_annot",
      "class": [
        "musica"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "musica_sbs96",
      "title": "musica_sbs96",
      "object": "musica_sbs96",
      "class": [
        "musica"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "musica_sbs96_tiny",
      "title": "musica_sbs96_tiny",
      "object": "musica_sbs96_tiny",
      "class": [
        "musica"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "rep_range",
      "title": "Replication Timing Data as GRanges Object",
      "object": "rep_range",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "res",
      "title": "res",
      "object": "res",
      "class": [
        "musica"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "res_annot",
      "title": "res_annot",
      "object": "res_annot",
      "class": [
        "musica"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "add_flank_to_variants",
      "title": "Uses a genome object to find context and add it to the variant table",
      "topics": [
        "add_flank_to_variants"
      ]
    },
    {
      "page": "add_result",
      "title": "Load an external model into a musica object",
      "topics": [
        "add_result"
      ]
    },
    {
      "page": "annotate_replication_strand",
      "title": "Add replication strand annotation to SBS variants based on bedgraph file",
      "topics": [
        "annotate_replication_strand"
      ]
    },
    {
      "page": "annotate_transcript_strand",
      "title": "Add transcript strand annotation to SBS variants (defined in genes only)",
      "topics": [
        "annotate_transcript_strand"
      ]
    },
    {
      "page": "annotate_variant_length",
      "title": "Adds an annotation to the input musica's variant table with length of each variant",
      "topics": [
        "annotate_variant_length"
      ]
    },
    {
      "page": "annotate_variant_type",
      "title": "Annotate variants with variant type (\"SBS\", \"INS\", \"DEl\", \"DBS\")",
      "topics": [
        "annotate_variant_type"
      ]
    },
    {
      "page": "auto_predict_grid",
      "title": "Automatic filtering of signatures for exposure prediction gridded across specific annotation",
      "topics": [
        "auto_predict_grid"
      ]
    },
    {
      "page": "build_custom_table",
      "title": "Builds a custom table from specified user variants",
      "topics": [
        "build_custom_table"
      ]
    },
    {
      "page": "build_standard_table",
      "title": "Builds count tables using various mutation type schemas",
      "topics": [
        "build_standard_table"
      ]
    },
    {
      "page": "built_tables",
      "title": "Retrieve the names of count_tables from a musica object",
      "topics": [
        "built_tables",
        "built_tables,musica-method"
      ]
    },
    {
      "page": "cluster_exposure",
      "title": "Perform clustering analysis from a musica result object",
      "topics": [
        "cluster_exposure"
      ]
    },
    {
      "page": "combine_count_tables",
      "title": "Combines tables into a single table that can be used for discovery/prediction",
      "topics": [
        "combine_count_tables"
      ]
    },
    {
      "page": "combine_predict_grid",
      "title": "Combine signatures and exposures of different models. Exposure values are zero for samples in an annotation where that signature was not predicted",
      "topics": [
        "combine_predict_grid"
      ]
    },
    {
      "page": "compare_cosmic_v2",
      "title": "Compare a result object to COSMIC V2 SBS Signatures (combination whole-exome and whole-genome)",
      "topics": [
        "compare_cosmic_v2"
      ]
    },
    {
      "page": "compare_cosmic_v3",
      "title": "Compare a result object to COSMIC V3 Signatures; Select exome or genome for SBS and only genome for DBS or Indel classes",
      "topics": [
        "compare_cosmic_v3"
      ]
    },
    {
      "page": "compare_k_vals",
      "title": "Compare k values",
      "topics": [
        "compare_k_vals"
      ]
    },
    {
      "page": "compare_results",
      "title": "Compare two result files to find similar signatures",
      "topics": [
        "compare_results"
      ]
    },
    {
      "page": "cosmic_v2_sigs",
      "title": "COSMIC v2 SBS96 Signatures Result Object",
      "topics": [
        "cosmic_v2_sigs"
      ]
    },
    {
      "page": "cosmic_v2_subtype_map",
      "title": "Input a cancer subtype to return a list of related COSMIC signatures",
      "topics": [
        "cosmic_v2_subtype_map"
      ]
    },
    {
      "page": "cosmic_v3_dbs_sigs",
      "title": "COSMIC v3 DBS Genome Signatures Result Object",
      "topics": [
        "cosmic_v3_dbs_sigs"
      ]
    },
    {
      "page": "cosmic_v3_indel_sigs",
      "title": "COSMIC v3 Indel Genome Signatures Result Object",
      "topics": [
        "cosmic_v3_indel_sigs"
      ]
    },
    {
      "page": "cosmic_v3_sbs_sigs",
      "title": "COSMIC v3 SBS96 Genome Signatures Result Object",
      "topics": [
        "cosmic_v3_sbs_sigs"
      ]
    },
    {
      "page": "cosmic_v3_sbs_sigs_exome",
      "title": "COSMIC v3 SBS96 Exome Signatures Result Object",
      "topics": [
        "cosmic_v3_sbs_sigs_exome"
      ]
    },
    {
      "page": "count_table-class",
      "title": "Object containing the count table matrices, their names and descriptions that we generated by provided and by user functions. These are used to discover and infer signatures and exposures.",
      "topics": [
        "count_table-class"
      ]
    },
    {
      "page": "create_musica_from_counts",
      "title": "Creates a musica object from a mutation count table",
      "topics": [
        "create_musica_from_counts"
      ]
    },
    {
      "page": "create_musica_from_variants",
      "title": "Creates a musica object from a variant table",
      "topics": [
        "create_musica_from_variants"
      ]
    },
    {
      "page": "create_umap",
      "title": "Create a UMAP from a model result",
      "topics": [
        "create_umap"
      ]
    },
    {
      "page": "credible_intervals",
      "title": "Retrieve credible_intervals from a result_model, result_collection, or musica object",
      "topics": [
        "credible_intervals",
        "credible_intervals,musica-method",
        "credible_intervals,result_collection-method",
        "credible_intervals,result_model-method",
        "credible_intervals<-",
        "credible_intervals<-,musica,matrix-method",
        "credible_intervals<-,result_collection,matrix-method",
        "credible_intervals<-,result_model,matrix-method"
      ]
    },
    {
      "page": "dbs_musica",
      "title": "dbs_musica",
      "topics": [
        "dbs_musica"
      ]
    },
    {
      "page": "discover_signatures",
      "title": "Discover mutational signatures",
      "topics": [
        "discover_signatures"
      ]
    },
    {
      "page": "drop_annotation",
      "title": "Drops a column from the variant table that the user no longer needs",
      "topics": [
        "drop_annotation"
      ]
    },
    {
      "page": "exposure_differential_analysis",
      "title": "Compare exposures of annotated samples",
      "topics": [
        "exposure_differential_analysis"
      ]
    },
    {
      "page": "exposures",
      "title": "Retrieve exposures from a result_model, result_collection, or musica object",
      "topics": [
        "exposures",
        "exposures,musica-method",
        "exposures,result_collection-method",
        "exposures,result_model-method",
        "exposures<-",
        "exposures<-,musica,matrix-method",
        "exposures<-,result_collection,matrix-method",
        "exposures<-,result_model,matrix-method"
      ]
    },
    {
      "page": "extract_count_tables",
      "title": "Extract count tables list from a musica object",
      "topics": [
        "extract_count_tables"
      ]
    },
    {
      "page": "extract_variants",
      "title": "Extract variants from mutliple objects",
      "topics": [
        "extract_variants"
      ]
    },
    {
      "page": "extract_variants_from_maf",
      "title": "Extract variants from a maf object",
      "topics": [
        "extract_variants_from_maf"
      ]
    },
    {
      "page": "extract_variants_from_maf_file",
      "title": "Extracts variants from a maf file",
      "topics": [
        "extract_variants_from_maf_file"
      ]
    },
    {
      "page": "extract_variants_from_matrix",
      "title": "Extract variants from matrix or data.frame like objects",
      "topics": [
        "extract_variants_from_matrix"
      ]
    },
    {
      "page": "extract_variants_from_vcf",
      "title": "Extracts variants from a VariantAnnotation VCF object",
      "topics": [
        "extract_variants_from_vcf"
      ]
    },
    {
      "page": "extract_variants_from_vcf_file",
      "title": "Extracts variants from a vcf file",
      "topics": [
        "extract_variants_from_vcf_file"
      ]
    },
    {
      "page": "generate_result_grid",
      "title": "Generate result_grid from musica based on annotation and range of k",
      "topics": [
        "generate_result_grid"
      ]
    },
    {
      "page": "get_count_table",
      "title": "Retrieve count_table matrix from count_table object",
      "topics": [
        "get_count_table"
      ]
    },
    {
      "page": "get_modality",
      "title": "Retrieve a specific modality entry from a musica or result_collection object",
      "topics": [
        "get_modality",
        "get_modality,musica-method",
        "get_modality,result_collection-method"
      ]
    },
    {
      "page": "get_model",
      "title": "Retrieve model from a musica or result collection object",
      "topics": [
        "get_model",
        "get_model,musica-method",
        "get_model,result_collection-method"
      ]
    },
    {
      "page": "get_result_list_entry",
      "title": "Retrieve result_list entry from a musica object",
      "topics": [
        "get_result_list_entry",
        "get_result_list_entry,musica,character-method"
      ]
    },
    {
      "page": "hyperparameter",
      "title": "Retrieve hyperparameter from a musica or result_collection object",
      "topics": [
        "hyperparameter",
        "hyperparameter,musica-method",
        "hyperparameter,result_collection-method",
        "hyperparameter<-",
        "hyperparameter<-,musica,list-method",
        "hyperparameter<-,result_collection,list-method"
      ]
    },
    {
      "page": "indel_musica",
      "title": "indel_musica",
      "topics": [
        "indel_musica"
      ]
    },
    {
      "page": "k_select",
      "title": "Plots for helping decide number of clusters",
      "topics": [
        "k_select"
      ]
    },
    {
      "page": "metrics",
      "title": "Retrieve metrics from a result_model, result_collection, or musica object",
      "topics": [
        "metrics",
        "metrics,musica-method",
        "metrics,result_collection-method",
        "metrics,result_model-method",
        "metrics<-",
        "metrics<-,musica,SimpleList-method",
        "metrics<-,result_collection,SimpleList-method",
        "metrics<-,result_model,SimpleList-method"
      ]
    },
    {
      "page": "modality",
      "title": "Retrieve modality from a result_model, result_collection, or musica object",
      "topics": [
        "modality",
        "modality,musica-method",
        "modality,result_collection-method",
        "modality,result_model-method",
        "modality<-",
        "modality<-,musica,matrix-method",
        "modality<-,result_collection,matrix-method",
        "modality<-,result_model,matrix-method"
      ]
    },
    {
      "page": "model_id",
      "title": "Retrieve model_id from a result_model, result_collection, or musica object",
      "topics": [
        "model_id",
        "model_id,musica-method",
        "model_id,result_collection-method",
        "model_id,result_model-method",
        "model_id<-",
        "model_id<-,musica,matrix-method",
        "model_id<-,result_collection,matrix-method",
        "model_id<-,result_model,matrix-method"
      ]
    },
    {
      "page": "musica",
      "title": "musica",
      "topics": [
        "musica"
      ]
    },
    {
      "page": "musica_annot",
      "title": "musica_annot",
      "topics": [
        "musica_annot"
      ]
    },
    {
      "page": "musica_sbs96",
      "title": "musica_sbs96",
      "topics": [
        "musica_sbs96"
      ]
    },
    {
      "page": "musica_sbs96_tiny",
      "title": "musica_sbs96_tiny",
      "topics": [
        "musica_sbs96_tiny"
      ]
    },
    {
      "page": "musica-class",
      "title": "The primary object that contains variants, count_tables, and samples annotations",
      "topics": [
        "musica-class"
      ]
    },
    {
      "page": "musicatk",
      "title": "Starts the musicatk interactive Shiny app",
      "topics": [
        "musicatk"
      ]
    },
    {
      "page": "name_signatures",
      "title": "Rename signatures for a model",
      "topics": [
        "name_signatures"
      ]
    },
    {
      "page": "num_signatures",
      "title": "Retrieve num_signatures from a result_model, result_collection, or musica object",
      "topics": [
        "num_signatures",
        "num_signatures,musica-method",
        "num_signatures,result_collection-method",
        "num_signatures,result_model-method",
        "num_signatures<-",
        "num_signatures<-,musica,matrix-method",
        "num_signatures<-,result_collection,matrix-method",
        "num_signatures<-,result_model,matrix-method"
      ]
    },
    {
      "page": "other_parameters",
      "title": "Retrieve other_parameters from a result_model, result_collection, or musica object",
      "topics": [
        "other_parameters",
        "other_parameters,musica-method",
        "other_parameters,result_collection-method",
        "other_parameters,result_model-method",
        "other_parameters<-",
        "other_parameters<-,musica,matrix-method",
        "other_parameters<-,result_collection,matrix-method",
        "other_parameters<-,result_model,matrix-method"
      ]
    },
    {
      "page": "parameter",
      "title": "Retrieve parameter from a musica or result_collection object",
      "topics": [
        "parameter",
        "parameter,musica-method",
        "parameter,result_collection-method",
        "parameter<-",
        "parameter<-,musica,list-method",
        "parameter<-,result_collection,list-method"
      ]
    },
    {
      "page": "plot_cluster",
      "title": "Visualize clustering results",
      "topics": [
        "plot_cluster"
      ]
    },
    {
      "page": "plot_differential_analysis",
      "title": "Compare exposures of annotated samples",
      "topics": [
        "plot_differential_analysis"
      ]
    },
    {
      "page": "plot_exposures",
      "title": "Display sample exposures with bar, box, or violin plots",
      "topics": [
        "plot_exposures"
      ]
    },
    {
      "page": "plot_heatmap",
      "title": "Plot heatmaps using the exposures matrix",
      "topics": [
        "plot_heatmap"
      ]
    },
    {
      "page": "plot_k_comparison",
      "title": "Plot k comparison",
      "topics": [
        "plot_k_comparison"
      ]
    },
    {
      "page": "plot_sample_counts",
      "title": "Plot distribution of sample counts",
      "topics": [
        "plot_sample_counts"
      ]
    },
    {
      "page": "plot_sample_reconstruction_error",
      "title": "Plot reconstruction error for a sample",
      "topics": [
        "plot_sample_reconstruction_error"
      ]
    },
    {
      "page": "plot_signatures",
      "title": "Plots the mutational signatures",
      "topics": [
        "plot_signatures"
      ]
    },
    {
      "page": "plot_umap",
      "title": "Plot a UMAP from a musica result",
      "topics": [
        "plot_umap"
      ]
    },
    {
      "page": "predict_exposure",
      "title": "Prediction of exposures in new samples using pre-existing signatures",
      "topics": [
        "predict_exposure"
      ]
    },
    {
      "page": "rc",
      "title": "Reverse complement of a string using biostrings",
      "topics": [
        "rc"
      ]
    },
    {
      "page": "rep_range",
      "title": "Replication Timing Data as GRanges Object",
      "topics": [
        "rep_range"
      ]
    },
    {
      "page": "res",
      "title": "res",
      "topics": [
        "res"
      ]
    },
    {
      "page": "res_annot",
      "title": "res_annot",
      "topics": [
        "res_annot"
      ]
    },
    {
      "page": "result_collection-class",
      "title": "The Result Collection object that contains modality, input parameters, prior hyperparameters",
      "topics": [
        "result_collection-class"
      ]
    },
    {
      "page": "result_list",
      "title": "Retrieve result_list from a musica object",
      "topics": [
        "result_list",
        "result_list,musica-method",
        "result_list<-",
        "result_list<-,musica,SimpleList-method"
      ]
    },
    {
      "page": "result_model-class",
      "title": "Object that contains results for a single model",
      "topics": [
        "result_model-class"
      ]
    },
    {
      "page": "samp_annot",
      "title": "Get or set sample annotations from a musica object",
      "topics": [
        "samp_annot",
        "samp_annot,musica-method",
        "samp_annot<-",
        "samp_annot<-,musica,character,vector-method"
      ]
    },
    {
      "page": "sample_names",
      "title": "Retrieve sample names from a musica object",
      "topics": [
        "sample_names",
        "sample_names,musica-method"
      ]
    },
    {
      "page": "select_genome",
      "title": "Helper function to load common human or mouse genomes",
      "topics": [
        "select_genome"
      ]
    },
    {
      "page": "signatures",
      "title": "Retrieve signatures from a result_model, result_collection, or musica object",
      "topics": [
        "signatures",
        "signatures,musica-method",
        "signatures,result_collection-method",
        "signatures,result_model-method",
        "signatures<-",
        "signatures<-,musica,matrix-method",
        "signatures<-,result_collection,matrix-method",
        "signatures<-,result_model,matrix-method"
      ]
    },
    {
      "page": "subset_musica_by_annotation",
      "title": "Creates a new musica object subsetted to only one value of a sample annotation",
      "topics": [
        "subset_musica_by_annotation"
      ]
    },
    {
      "page": "subset_musica_by_counts",
      "title": "Creates a new musica subsetted to only samples with enough variants",
      "topics": [
        "subset_musica_by_counts"
      ]
    },
    {
      "page": "subset_variant_by_type",
      "title": "Subsets a variant table based on Variant Type",
      "topics": [
        "subset_variant_by_type"
      ]
    },
    {
      "page": "subset_variants_by_samples",
      "title": "Return sample from musica_variant object",
      "topics": [
        "subset_variants_by_samples"
      ]
    },
    {
      "page": "table_selected",
      "title": "Retrieve table name used for plotting from a result_model object",
      "topics": [
        "table_selected",
        "table_selected,result_model-method"
      ]
    },
    {
      "page": "tables",
      "title": "Retrieve the list of count_tables from a musica object",
      "topics": [
        "tables",
        "tables,musica-method",
        "tables<-",
        "tables<-,musica,list-method"
      ]
    },
    {
      "page": "umap",
      "title": "Retrieve umap list from a result_model, result_collection, or musica object",
      "topics": [
        "umap",
        "umap,musica-method",
        "umap,result_collection-method",
        "umap,result_model-method",
        "umap<-",
        "umap<-,musica,matrix-method",
        "umap<-,result_collection,matrix-method",
        "umap<-,result_model,matrix-method"
      ]
    },
    {
      "page": "variants",
      "title": "Retrieve variants from a musica object",
      "topics": [
        "variants",
        "variants,musica-method",
        "variants<-",
        "variants<-,musica,data.table-method"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/musicatk/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "askpass",
    "backports",
    "base64enc",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocIO",
    "BiocManager",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "boot",
    "broom",
    "BSgenome",
    "BSgenome.Hsapiens.UCSC.hg19",
    "BSgenome.Hsapiens.UCSC.hg38",
    "BSgenome.Mmusculus.UCSC.mm10",
    "BSgenome.Mmusculus.UCSC.mm9",
    "bslib",
    "cachem",
    "callr",
    "car",
    "carData",
    "cellranger",
    "cigarillo",
    "circlize",
    "cli",
    "clipr",
    "clue",
    "cluster",
    "codetools",
    "colorspace",
    "combinat",
    "commonmark",
    "ComplexHeatmap",
    "conflicted",
    "corrplot",
    "cowplot",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "decompTumor2Sig",
    "DelayedArray",
    "dendextend",
    "Deriv",
    "digest",
    "DNAcopy",
    "doBy",
    "doParallel",
    "dplyr",
    "dqrng",
    "DT",
    "dtplyr",
    "ellipse",
    "emmeans",
    "estimability",
    "evaluate",
    "factoextra",
    "FactoMineR",
    "farver",
    "fastmap",
    "flashClust",
    "FNN",
    "fontawesome",
    "forcats",
    "foreach",
    "forecast",
    "formatR",
    "Formula",
    "fracdiff",
    "fs",
    "futile.logger",
    "futile.options",
    "gargle",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "GetoptLong",
    "ggplot2",
    "ggpubr",
    "ggrepel",
    "ggsci",
    "ggseqlogo",
    "ggsignif",
    "GlobalOptions",
    "glue",
    "googledrive",
    "googlesheets4",
    "gridBase",
    "gridExtra",
    "gtable",
    "gtools",
    "haven",
    "highr",
    "hms",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr",
    "ids",
    "IRanges",
    "irlba",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "KernSmooth",
    "knitr",
    "labeling",
    "lambda.r",
    "later",
    "lattice",
    "lazyeval",
    "leaps",
    "lifecycle",
    "lme4",
    "lmtest",
    "lubridate",
    "maftools",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "MatrixModels",
    "matrixStats",
    "matrixTests",
    "MCMCprecision",
    "memoise",
    "mgcv",
    "microbenchmark",
    "mime",
    "minqa",
    "modelr",
    "modeltools",
    "multcompView",
    "mvtnorm",
    "nlme",
    "nloptr",
    "NLP",
    "NMF",
    "nnet",
    "numDeriv",
    "openssl",
    "otel",
    "pbkrtest",
    "pheatmap",
    "philentropy",
    "pillar",
    "pkgconfig",
    "plotly",
    "plyr",
    "png",
    "polynom",
    "poorman",
    "prettyunits",
    "processx",
    "progress",
    "promises",
    "ps",
    "purrr",
    "quadprog",
    "quantreg",
    "R6",
    "ragg",
    "rappdirs",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppAnnoy",
    "RcppArmadillo",
    "RcppEigen",
    "RcppParallel",
    "RcppProgress",
    "RCurl",
    "Rdpack",
    "readr",
    "readxl",
    "reformulas",
    "registry",
    "rematch",
    "rematch2",
    "reprex",
    "reshape2",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "rmarkdown",
    "rngtools",
    "Rsamtools",
    "RSpectra",
    "RSQLite",
    "rstatix",
    "rstudioapi",
    "rtracklayer",
    "rvest",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "scatterplot3d",
    "selectr",
    "Seqinfo",
    "shape",
    "shiny",
    "sitmo",
    "slam",
    "snow",
    "sourcetools",
    "SparseArray",
    "SparseM",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sys",
    "systemfonts",
    "textshaping",
    "tibble",
    "tidyr",
    "tidyselect",
    "tidyverse",
    "timechange",
    "timeDate",
    "tinytex",
    "tm",
    "topicmodels",
    "TxDb.Hsapiens.UCSC.hg19.knownGene",
    "TxDb.Hsapiens.UCSC.hg38.knownGene",
    "tzdb",
    "UCSC.utils",
    "urca",
    "utf8",
    "uuid",
    "uwot",
    "VariantAnnotation",
    "vctrs",
    "viridis",
    "viridisLite",
    "vroom",
    "withr",
    "xfun",
    "XML",
    "xml2",
    "xtable",
    "XVector",
    "yaml",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "musicatk.Rmd",
      "filename": "musicatk.html",
      "title": "Mutational Signature Comprehensive Analysis Toolkit",
      "author": "Aaron Chevalier, Joshua Campbell",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Vignettes",
        "Introduction",
        "Installation",
        "Setting up a musica object",
        "Extracting variants",
        "Choosing a genome",
        "Creating a musica object",
        "Creating mutation count tables",
        "Creating a musica object directly from a count table",
        "Discovering Signatures and Exposures",
        "Determining an appropriate k value",
        "Plotting",
        "Signatures",
        "Exposures",
        "Comparison to external signatures (e.g. COSMIC)",
        "Predicting exposures using pre-existing signatures",
        "Comparing samples between groups using Sample Annotations",
        "Adding sample annotations",
        "Plotting exposures by a Sample Annotation",
        "Visualizing samples in 2D using UMAP",
        "Use of Plotly in plotting",
        "Note on reproducibility",
        "Session Information"
      ],
      "created": "2020-10-02 04:09:47",
      "modified": "2025-07-16 00:29:04",
      "commits": 15
    }
  ],
  "_score": 6.681241237375588,
  "_indexed": true,
  "_nocasepkg": "musicatk",
  "_universes": [
    "bioc",
    "camplab",
    "campbio"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.7.0",
      "date": "2026-05-30T10:22:13.000Z",
      "distro": "noble",
      "commit": "4eabe7f8aecc2a4490cd6b60178b9db348a92d5c",
      "fileid": "1fa3c4125c3e59d6a7f77b9402341e7879b25248d11668b12b4ccaf4f9519e7b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675586046"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.7.0",
      "date": "2026-05-30T10:23:03.000Z",
      "distro": "noble",
      "commit": "4eabe7f8aecc2a4490cd6b60178b9db348a92d5c",
      "fileid": "7c56eb821c17cc51dc8d53f9a3a165c7aacf395e37c53cfb8ec739d92877ea34",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675586046"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.7.0",
      "date": "2026-05-30T14:29:28.000Z",
      "commit": "4eabe7f8aecc2a4490cd6b60178b9db348a92d5c",
      "fileid": "c5947703c80a5fe50a7a45abc14d6ebab8a873a377b96112aed1cf0d91aa59bd",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675586046"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.7.0",
      "date": "2026-05-30T14:26:14.000Z",
      "commit": "4eabe7f8aecc2a4490cd6b60178b9db348a92d5c",
      "fileid": "d4e623e234742fe8c9b0e1c46e771f52822fd9cb7e7e7c8212fb787a9531213f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675586046"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.7.0",
      "date": "2026-05-30T10:18:45.000Z",
      "commit": "4eabe7f8aecc2a4490cd6b60178b9db348a92d5c",
      "fileid": "3d3a3fe3b95c1bb00d8e16810884f364ba1403aa6394aaff62334e3159a93a2b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675586046"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.7.0",
      "date": "2026-05-30T10:19:09.000Z",
      "commit": "4eabe7f8aecc2a4490cd6b60178b9db348a92d5c",
      "fileid": "bea208c4d5cabb43b530ad0f532397b53df5c2e2515ab1cbcae9b2fe28a128a1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675586046"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.7.0",
      "date": "2026-05-30T10:18:55.000Z",
      "commit": "4eabe7f8aecc2a4490cd6b60178b9db348a92d5c",
      "fileid": "c247e0cf0eecc812be86248d9abdee3575a70136b73b9504efb02d4cdbbd2bf2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675586046"
    }
  ]
}