{
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  "Package": "mSigSpectra",
  "Type": "Package",
  "Title": "Build Mutational-Spectrum Catalogs from Variant Call Format\nFiles",
  "Version": "0.1.3",
  "Authors@R": "c(person(given = \"Steve\",\nfamily = \"Rozen\",\nrole = c(\"aut\", \"cre\"),\nemail = \"steverozen@pm.me\"),\nperson(given = \"Nanhai\",\nfamily = \"Jiang\",\nrole = \"aut\"),\nperson(given = \"Arnoud\",\nfamily = \"Boot\",\nrole = \"aut\"),\nperson(given = \"Mo\",\nfamily = \"Liu\",\nrole = \"aut\"),\nperson(given = \"Yang\",\nfamily = \"Wu\",\nrole = \"aut\"),\nperson(given = c(\"Mi\", \"Ni\"),\nfamily = \"Huang\",\nrole = \"aut\"),\nperson(given = c(\"Jia\", \"Geng\"),\nfamily = \"Chang\",\nrole = \"aut\"))",
  "Description": "Reads variant call format (VCF) files in a caller-agnostic\nway, annotates variants with flanking sequence context and\ntranscriptional strand, and builds mutational-spectrum catalogs\nof single base substitutions (SBS), doublet base substitutions\n(DBS), and small insertions and deletions (indels, ID) at\nseveral resolutions (SBS96, SBS192, SBS1536, DBS78, DBS136,\nDBS144, ID83, ID89, ID166, ID476) and in both counts and\ndensity representations. Successor to the numerical core of the\n'ICAMS' package with plotting, 'shiny', and portable document\nformat (PDF) reporting removed; plotting is provided separately\nby 'mSigPlot'. Used in the preparation of Rozen et al. (2026)\n<doi:10.5281/zenodo.18451842>.",
  "License": "GPL-3",
  "URL": "https://github.com/steverozen/mSigSpectra,\nhttps://steverozen.github.io/mSigSpectra/",
  "BugReports": "https://github.com/steverozen/mSigSpectra/issues",
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  "Repository": "https://steverozen.r-universe.dev",
  "Date/Publication": "2026-09-16 17:38:58 UTC",
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  "Author": "Steve Rozen [aut, cre],\nNanhai Jiang [aut],\nArnoud Boot [aut],\nMo Liu [aut],\nYang Wu [aut],\nMi Ni Huang [aut],\nJia Geng Chang [aut]",
  "Maintainer": "Steve Rozen <steverozen@pm.me>",
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  "_created": "2026-10-11T11:17:26.000Z",
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    "annot_vcf_to_476_catalog",
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    "annot_vcf_to_89_catalog",
    "annotate_id_vcf",
    "annotate_sbs_or_dbs_vcf",
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    "catalog_attrs",
    "catalog_row_order",
    "categorize_1_justified_indel",
    "cbind_catalogs",
    "change_476_type_ids_to_open_intervals",
    "change_89_type_ids_to_open_intervals",
    "check_and_remove_discarded_variants",
    "collapse_catalog",
    "infer_trans_ranges",
    "is_catalog",
    "justify_id_vcf",
    "justify_indel",
    "read_catalog",
    "read_vcf",
    "read_vcfs",
    "seg_simple",
    "segment_simple_cpp",
    "split_vcf",
    "subset_catalog",
    "transform_catalog",
    "vcf_to_dbs_catalog",
    "vcf_to_id_catalog",
    "vcf_to_sbs_catalog",
    "write_catalog"
  ],
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      "fields": [],
      "table": false,
      "tojson": true
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      "table": true,
      "tojson": true
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      "title": "Transcript ranges for transcriptional strand annotation",
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        "data.frame"
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        "end",
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      "table": true,
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      "name": "trans.ranges.GRCm38",
      "title": "Transcript ranges for transcriptional strand annotation",
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        "data.frame"
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        "start",
        "end",
        "strand",
        "Ensembl.gene.ID",
        "gene.symbol"
      ],
      "rows": 20325,
      "table": true,
      "tojson": true
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  "_help": [
    {
      "page": "add_seq_context",
      "title": "Add flanking sequence context to a VCF data frame",
      "topics": [
        "add_seq_context"
      ]
    },
    {
      "page": "add_transcript_strand",
      "title": "Annotate a VCF data frame with transcript strand information",
      "topics": [
        "add_transcript_strand"
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    },
    {
      "page": "all.abundance",
      "title": "K-mer abundances for density calculations",
      "topics": [
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    },
    {
      "page": "annot_vcf_to_476_catalog",
      "title": "Convert an annotated indel VCF to a Koh 476-category catalog",
      "topics": [
        "annot_vcf_to_476_catalog"
      ]
    },
    {
      "page": "annot_vcf_to_83_catalog",
      "title": "Convert an annotated indel VCF to a COSMIC 83-category catalog",
      "topics": [
        "annot_vcf_to_83_catalog"
      ]
    },
    {
      "page": "annot_vcf_to_89_catalog",
      "title": "Convert an annotated indel VCF to a Koh 89-category catalog",
      "topics": [
        "annot_vcf_to_89_catalog"
      ]
    },
    {
      "page": "annotate_id_vcf",
      "title": "Annotate an in-memory ID (indel) VCF with sequence context, transcript strand, and COSMIC / Koh indel categories",
      "topics": [
        "annotate_id_vcf"
      ]
    },
    {
      "page": "annotate_sbs_or_dbs_vcf",
      "title": "Annotate an SBS or DBS VCF with flanking sequence context and transcript strand",
      "topics": [
        "annotate_sbs_or_dbs_vcf"
      ]
    },
    {
      "page": "as_catalog",
      "title": "Turn a numeric matrix into a mutational-spectrum catalog",
      "topics": [
        "as_catalog"
      ]
    },
    {
      "page": "catalog_attrs",
      "title": "Report the attributes of an mSigSpectra catalog",
      "topics": [
        "catalog_attrs"
      ]
    },
    {
      "page": "catalog_row_order",
      "title": "Return catalog row orders for all supported catalog types",
      "topics": [
        "catalog_row_order"
      ]
    },
    {
      "page": "categorize_1_justified_indel",
      "title": "Given a indel and its sequence context, categorize it",
      "topics": [
        "categorize_1_justified_indel"
      ]
    },
    {
      "page": "cbind_catalogs",
      "title": "Combine catalogs across samples (column-bind)",
      "topics": [
        "cbind_catalogs"
      ]
    },
    {
      "page": "change_476_type_ids_to_open_intervals",
      "title": "Change 476-type indel category identifiers to use right-open repeat intervals",
      "topics": [
        "change_476_type_ids_to_open_intervals"
      ]
    },
    {
      "page": "change_89_type_ids_to_open_intervals",
      "title": "Change 89-type indel category identifiers to use right-open repeat intervals",
      "topics": [
        "change_89_type_ids_to_open_intervals"
      ]
    },
    {
      "page": "check_and_remove_discarded_variants",
      "title": "Check a VCF for common variant-level problems and remove the offenders",
      "topics": [
        "check_and_remove_discarded_variants"
      ]
    },
    {
      "page": "collapse_catalog",
      "title": "Collapse a higher-resolution catalog to a lower-resolution one",
      "topics": [
        "collapse_catalog"
      ]
    },
    {
      "page": "infer_trans_ranges",
      "title": "Infer transcript ranges for a reference genome",
      "topics": [
        "infer_trans_ranges"
      ]
    },
    {
      "page": "is_catalog",
      "title": "Check whether an object looks like an mSigSpectra catalog",
      "topics": [
        "is_catalog"
      ]
    },
    {
      "page": "justify_id_vcf",
      "title": "Add sequence context and transcript information to an in-memory ID (insertion/deletion) VCF, and confirm that they match the given reference genome",
      "topics": [
        "justify_id_vcf"
      ]
    },
    {
      "page": "justify_indel",
      "title": "Move the notional position of a deletion or insertion as far left as possible.",
      "topics": [
        "justify_indel"
      ]
    },
    {
      "page": "read_catalog",
      "title": "Read a mutational-spectrum catalog from a file",
      "topics": [
        "read_catalog"
      ]
    },
    {
      "page": "read_vcf",
      "title": "Read a VCF file into a data.table, caller-agnostically",
      "topics": [
        "read_vcf"
      ]
    },
    {
      "page": "read_vcfs",
      "title": "Read multiple VCF files",
      "topics": [
        "read_vcfs"
      ]
    },
    {
      "page": "seg_simple",
      "title": "Segment a single indel sequence using Rcpp interface",
      "topics": [
        "seg_simple"
      ]
    },
    {
      "page": "segment_simple_cpp",
      "title": "Segment a single indel using Rcpp interface",
      "topics": [
        "segment_simple_cpp"
      ]
    },
    {
      "page": "split_vcf",
      "title": "Split a mixed-mutation VCF into SBS / DBS / ID sub-tables",
      "topics": [
        "split_vcf"
      ]
    },
    {
      "page": "subset_catalog",
      "title": "Subset a catalog while preserving attributes",
      "topics": [
        "subset_catalog"
      ]
    },
    {
      "page": "trans.ranges",
      "title": "Transcript ranges for transcriptional strand annotation",
      "topics": [
        "trans.ranges",
        "trans.ranges.GRCh37",
        "trans.ranges.GRCh38",
        "trans.ranges.GRCm38"
      ]
    },
    {
      "page": "transform_catalog",
      "title": "Transform a catalog between counts and density",
      "topics": [
        "transform_catalog"
      ]
    },
    {
      "page": "vcf_to_dbs_catalog",
      "title": "Build a DBS mutational-spectrum catalog from an annotated DBS VCF",
      "topics": [
        "vcf_to_dbs_catalog"
      ]
    },
    {
      "page": "vcf_to_id_catalog",
      "title": "Build an ID (indel) mutational-spectrum catalog from an annotated ID VCF",
      "topics": [
        "vcf_to_id_catalog"
      ]
    },
    {
      "page": "vcf_to_sbs_catalog",
      "title": "Build an SBS mutational-spectrum catalog from an annotated SBS VCF",
      "topics": [
        "vcf_to_sbs_catalog"
      ]
    },
    {
      "page": "write_catalog",
      "title": "Write a mutational-spectrum catalog to a file",
      "topics": [
        "write_catalog"
      ]
    }
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      "title": "Reading VCFs and Building Mutational-Spectrum Catalogs",
      "engine": "knitr::rmarkdown",
      "headings": [
        "1. Load packages",
        "2. Locate test VCFs",
        "3. Read the SBS VCF",
        "4. Split into SBS / DBS / ID sub-tables",
        "5. Annotate the SBS rows",
        "6. Build SBS catalogs",
        "7. Plot SBS catalogs",
        "8. Build and plot ID catalogs",
        "9. Counts ↔ density",
        "10. Collapse from finer to coarser resolutions",
        "11. Catalog I/O",
        "See also"
      ],
      "created": "2026-04-21 01:22:07",
      "modified": "2026-05-07 22:39:34",
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