{
  "_id": "6a1ae7b91d7bb097a09f1633",
  "Package": "transmogR",
  "Type": "Package",
  "Title": "Modify a set of reference sequences using a set of variants",
  "Version": "1.9.0",
  "Authors@R": "person(\"Stevie\", \"Pederson\", \nemail = \"stephen.pederson.au@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-8197-3303\")\n)",
  "Description": "transmogR provides the tools needed to crate a new\nreference genome or reference transcriptome, using a set of\nvariants. Variants can be any combination of SNPs, Insertions\nand Deletions. The intended use-case is to enable creation of\nvariant-modified reference transcriptomes for incorporation\ninto transcriptomic pseudo-alignment workflows, such as salmon.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "URL": "https://github.com/smped/transmogR",
  "BugReports": "https://github.com/smped/transmogR/issues",
  "biocViews": "Alignment, GenomicVariation, Sequencing,\nTranscriptomeVariant, VariantAnnotation",
  "BiocType": "Software",
  "VignetteBuilder": "knitr",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libpng-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:02:21 UTC",
  "RemoteUrl": "https://github.com/bioc/transmogR",
  "RemoteRef": "HEAD",
  "RemoteSha": "2035130cc4f17b9bc899cb51ca590850d68730b7",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-30 09:36:37 UTC",
    "User": "root"
  },
  "Author": "Stevie Pederson [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-8197-3303>)",
  "Maintainer": "Stevie Pederson <stephen.pederson.au@gmail.com>",
  "MD5sum": "74eebd6e006f8ea121270edf48d322fa",
  "_user": "bioc",
  "_type": "src",
  "_file": "transmogR_1.9.0.tar.gz",
  "_fileid": "7dc17cf09aa44ce4ceab37d8fb9d027418c2ed57a992785cbd2c0c0ebad7a380",
  "_filesize": 523423,
  "_sha256": "7dc17cf09aa44ce4ceab37d8fb9d027418c2ed57a992785cbd2c0c0ebad7a380",
  "_created": "2026-05-30T09:36:37.000Z",
  "_published": "2026-05-30T13:35:53.932Z",
  "_jobs": [
    {
      "job": 78640107543,
      "time": 256,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307340519"
    },
    {
      "job": 78640107598,
      "time": 411,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307271612"
    },
    {
      "job": 78640107587,
      "time": 528,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307365824"
    },
    {
      "job": 78640107603,
      "time": 415,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307271981"
    },
    {
      "job": 78640107585,
      "time": 545,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307367410"
    },
    {
      "job": 78640107566,
      "time": 309,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7308555946"
    },
    {
      "job": 78640107559,
      "time": 814,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307320098"
    },
    {
      "job": 78640107557,
      "time": 300,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7308555657"
    },
    {
      "job": 78640107568,
      "time": 803,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307319391"
    },
    {
      "job": 78639263065,
      "time": 512,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307229688"
    },
    {
      "job": 78640107540,
      "time": 210,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 78640107571,
      "time": 418,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307353382"
    },
    {
      "job": 78640107599,
      "time": 424,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307353862"
    },
    {
      "job": 78640107564,
      "time": 334,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307345497"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 5
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26675639796",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/transmogR",
  "_commit": {
    "id": "2035130cc4f17b9bc899cb51ca590850d68730b7",
    "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": 1777381341
  },
  "_maintainer": {
    "name": "Stevie Pederson",
    "email": "stephen.pederson.au@gmail.com",
    "login": "smped",
    "bluesky": "@smped.bsky.social",
    "description": "",
    "uuid": 8252496,
    "orcid": "0000-0001-8197-3303"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "Biostrings",
      "role": "Depends"
    },
    {
      "package": "GenomicRanges",
      "role": "Depends"
    },
    {
      "package": "BSgenome",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "Seqinfo",
      "role": "Imports"
    },
    {
      "package": "GenomicFeatures",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "version": ">= 4.0.0",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "patchwork",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "VariantAnnotation",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "BSgenome.Hsapiens.UCSC.hg38",
      "role": "Suggests"
    },
    {
      "package": "edgeR",
      "role": "Suggests"
    },
    {
      "package": "extraChIPs",
      "role": "Suggests"
    },
    {
      "package": "InteractionSet",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "readr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "rtracklayer",
      "role": "Suggests"
    },
    {
      "package": "SimpleUpset",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-38",
      "n": 1
    },
    {
      "week": "2025-40",
      "n": 2
    },
    {
      "week": "2025-41",
      "n": 3
    },
    {
      "week": "2025-43",
      "n": 3
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.9.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.8.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "alignment",
    "genomicvariation",
    "sequencing",
    "transcriptomevariant",
    "variantannotation",
    "zlib"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "smped",
      "count": 112,
      "uuid": 8252496
    },
    {
      "user": "jwokaty",
      "count": 10,
      "uuid": 1744257
    },
    {
      "user": "hpages",
      "count": 1,
      "uuid": 8810451
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 262,
    "source": "https://www.bioconductor.org/packages/stats/bioc/transmogR"
  },
  "_devurl": "https://github.com/smped/transmogr",
  "_searchresults": 6,
  "_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/transmogR.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/smped/transmogr",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "cleanVariants",
    "digestSalmon",
    "genomogrify",
    "indelcator",
    "overdispFromBoots",
    "overlapsByVar",
    "owl",
    "parY",
    "shiftByVar",
    "sjFromExons",
    "transmogrify",
    "upsetVarByCol",
    "varTags",
    "varTypes"
  ],
  "_help": [
    {
      "page": "cleanVariants-methods",
      "title": "Check provided variants for compatibility",
      "topics": [
        "cleanVariants",
        "cleanVariants,GRanges-method",
        "cleanVariants,VcfFile-method",
        "cleanVariants-methods"
      ]
    },
    {
      "page": "digestSalmon",
      "title": "Parse the output from salmon",
      "topics": [
        "digestSalmon",
        "overdispFromBoots"
      ]
    },
    {
      "page": "genomogrify-methods",
      "title": "Mogrify a genome using a set of variants",
      "topics": [
        "genomogrify",
        "genomogrify,BSgenome,GRanges-method",
        "genomogrify,BSgenome,VcfFile-method",
        "genomogrify,XStringSet,GRanges-method",
        "genomogrify,XStringSet,VcfFile-method",
        "genomogrify-methods"
      ]
    },
    {
      "page": "indelcator-methods",
      "title": "Substitute InDels into one or more sequences",
      "topics": [
        "indelcator",
        "indelcator,BSgenome,GRanges-method",
        "indelcator,DNAStringSet,GRanges-method",
        "indelcator,XString,GRanges-method"
      ]
    },
    {
      "page": "overlapsByVar-methods",
      "title": "Count overlaps by variant type",
      "topics": [
        "overlapsByVar",
        "overlapsByVar,GRanges,GRanges-method",
        "overlapsByVar,GRangesList,GRanges-method",
        "overlapsByVar-methods"
      ]
    },
    {
      "page": "owl-methods",
      "title": "OverWrite Letters in an XStringSet",
      "topics": [
        "owl",
        "owl,BSgenome,GRanges-method",
        "owl,XStringSet,GRanges-method"
      ]
    },
    {
      "page": "parY-methods",
      "title": "Get the PAR-Y Regions From a Seqinfo Object",
      "topics": [
        "parY",
        "parY,character-method",
        "parY,Seqinfo-method",
        "parY-methods"
      ]
    },
    {
      "page": "shiftByVar",
      "title": "Calculate new exon co-ordinates",
      "topics": [
        "shiftByVar"
      ]
    },
    {
      "page": "sjFromExons",
      "title": "Obtain Splice-Junctions from Exons and Transcripts",
      "topics": [
        "sjFromExons"
      ]
    },
    {
      "page": "transmogrify-methods",
      "title": "Mogrify a transcriptome using a set of variants",
      "topics": [
        "transmogrify",
        "transmogrify,BSgenome,GRanges,GRanges-method",
        "transmogrify,BSgenome,VcfFile,GRanges-method",
        "transmogrify,XStringSet,GRanges,GRanges-method",
        "transmogrify,XStringSet,VcfFile,GRanges-method",
        "transmogrify-methods"
      ]
    },
    {
      "page": "upsetVarByCol",
      "title": "Show Variants by Impacted Columns",
      "topics": [
        "upsetVarByCol"
      ]
    },
    {
      "page": "varTags",
      "title": "Create a set of tags indicating overlap status with variants",
      "topics": [
        "varTags"
      ]
    },
    {
      "page": "varTypes",
      "title": "Identify SNVs, Insertions and Deletions",
      "topics": [
        "varTypes"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/transmogR/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "askpass",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "BSgenome",
    "cachem",
    "cigarillo",
    "cli",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "DelayedArray",
    "farver",
    "fastmap",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "httr",
    "IRanges",
    "isoband",
    "jsonlite",
    "KEGGREST",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "openssl",
    "patchwork",
    "pkgconfig",
    "png",
    "R6",
    "RColorBrewer",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "rlang",
    "Rsamtools",
    "RSQLite",
    "rtracklayer",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "SummarizedExperiment",
    "sys",
    "VariantAnnotation",
    "vctrs",
    "viridisLite",
    "withr",
    "XML",
    "XVector",
    "yaml"
  ],
  "_sysdeps": [
    {
      "shlib": "libz",
      "package": "zlib1g",
      "headers": "zlib1g-dev",
      "source": "zlib",
      "version": "1:1.3.dfsg-3.1ubuntu2.1",
      "name": "zlib",
      "homepage": "http://zlib.net/",
      "description": "compression library - runtime"
    }
  ],
  "_vignettes": [
    {
      "source": "creating_a_new_reference.Rmd",
      "filename": "creating_a_new_reference.html",
      "title": "Creating a Variant-Modified Reference",
      "author": "Stevie Pederson",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Setup",
        "Installation",
        "Required Data",
        "Inspecting Variants",
        "Creating Modified Reference Sequences",
        "Modifying a Reference Transcriptome",
        "Modifying a Reference Genome",
        "Finding Modified Co-ordinates",
        "Additional Capabilities",
        "Pseudo-Autosomal Regions (PAR-Y)",
        "Splice Junctions",
        "Session info",
        "References"
      ],
      "created": "2024-01-09 08:00:54",
      "modified": "2025-10-03 14:46:07",
      "commits": 17
    }
  ],
  "_score": 4.778151250383644,
  "_indexed": true,
  "_nocasepkg": "transmogr",
  "_universes": [
    "bioc",
    "smped"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.9.0",
      "date": "2026-05-30T09:40:47.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "2035130cc4f17b9bc899cb51ca590850d68730b7",
      "fileid": "a8af13f2698f3f10425517b74020aa1481fb1b22c3ae51a5e2d52d54aef852b5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675639796"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.9.0",
      "date": "2026-05-30T09:56:03.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "2035130cc4f17b9bc899cb51ca590850d68730b7",
      "fileid": "9c5f6b9933e35012937e57dc8bd547f16d9cc2aa7dc0ef26b3cfc8501ab0cb68",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675639796"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.9.0",
      "date": "2026-05-30T09:41:00.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "2035130cc4f17b9bc899cb51ca590850d68730b7",
      "fileid": "62dc60db62494f0414ead9557824b556b64c602e47362f9a883128f81763eed8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675639796"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.9.0",
      "date": "2026-05-30T09:56:16.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "2035130cc4f17b9bc899cb51ca590850d68730b7",
      "fileid": "a88462ddfd00457e556a07c6b420e1cae66d6c6c1386aab2377c0cf98325430e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675639796"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.9.0",
      "date": "2026-05-30T13:32:23.000Z",
      "arch": "aarch64",
      "commit": "2035130cc4f17b9bc899cb51ca590850d68730b7",
      "fileid": "d3061438e0d3364cd5d11c7c8d93a32773b8655513eccc5fd6a33e6e140ff925",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675639796"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.9.0",
      "date": "2026-05-30T09:45:27.000Z",
      "arch": "x86_64",
      "commit": "2035130cc4f17b9bc899cb51ca590850d68730b7",
      "fileid": "a9a49f2f21355bd8b8cd8ac239a1175b3bac868f9f538a6bdf1dc452fdc53198",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675639796"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.9.0",
      "date": "2026-05-30T13:32:52.000Z",
      "arch": "aarch64",
      "commit": "2035130cc4f17b9bc899cb51ca590850d68730b7",
      "fileid": "a33ee5ef40a7c356ca90252564f88bdf3aad6149aa2f6132975addb148672209",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675639796"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.9.0",
      "date": "2026-05-30T09:44:13.000Z",
      "arch": "x86_64",
      "commit": "2035130cc4f17b9bc899cb51ca590850d68730b7",
      "fileid": "1ea939d1fb458201465d9dc3346c88405b2aee2426a594368cacaca27ecbacca",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675639796"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.9.0",
      "date": "2026-05-30T09:53:36.000Z",
      "arch": "x86_64",
      "commit": "2035130cc4f17b9bc899cb51ca590850d68730b7",
      "fileid": "b99803410eb0155f1e711774b738cdc0315803aeb4acb1f7b5f298cbb029a403",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675639796"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.9.0",
      "date": "2026-05-30T09:53:38.000Z",
      "arch": "x86_64",
      "commit": "2035130cc4f17b9bc899cb51ca590850d68730b7",
      "fileid": "7b53e72d507f16c503d98ae14024efe5b4b940b11d3ca868f2c310c106e59008",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675639796"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.9.0",
      "date": "2026-05-30T09:53:34.000Z",
      "arch": "x86_64",
      "commit": "2035130cc4f17b9bc899cb51ca590850d68730b7",
      "fileid": "35ddcf517744e2818600ac4109a563ba14162f063704edd043a1d86ee820f635",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675639796"
    }
  ]
}