{
  "_id": "6a1f1bb4b401979e7341f5f6",
  "Package": "VarCon",
  "Type": "Package",
  "Title": "VarCon: an R package for retrieving neighboring nucleotides of\nan SNV",
  "Version": "1.21.0",
  "Description": "VarCon is an R package which converts the positional\ninformation from the annotation of an single nucleotide\nvariation (SNV) (either referring to the coding sequence or the\nreference genomic sequence). It retrieves the genomic reference\nsequence around the position of the single nucleotide\nvariation. To asses, whether the SNV could potentially\ninfluence binding of splicing regulatory proteins VarCon\ncalcualtes the HEXplorer score as an estimation. Besides,\nVarCon additionally reports splice site strengths of splice\nsites within the retrieved genomic sequence and any changes due\nto the SNV.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "VignetteBuilder": "knitr",
  "biocViews": "FunctionalGenomics, AlternativeSplicing",
  "RoxygenNote": "7.1.1",
  "Authors@R": "person(\"Johannes\", \"Ptok\", role = c(\"aut\", \"cre\"), email = \"Johannes.Ptok@posteo.de\")",
  "Config/pak/sysreqs": "cmake make libbz2-dev liblzma-dev libuv1-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:54:30 UTC",
  "RemoteUrl": "https://github.com/bioc/VarCon",
  "RemoteRef": "HEAD",
  "RemoteSha": "b86f75b3dce88e5d10fb9c9c21a38c95075e1bd0",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-16 09:13:48 UTC",
    "User": "root"
  },
  "Author": "Johannes Ptok [aut, cre]",
  "Maintainer": "Johannes Ptok <Johannes.Ptok@posteo.de>",
  "MD5sum": "e455bac2454275189a886fdce3e00509",
  "_user": "bioc",
  "_type": "src",
  "_file": "VarCon_1.21.0.tar.gz",
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  "_filesize": 1906158,
  "_sha256": "59c66f8851a22440de7ee9373cc103cc3ecabc2cba93893c346727b83f14fa54",
  "_created": "2026-05-16T09:13:48.000Z",
  "_published": "2026-06-02T18:06:44.567Z",
  "_jobs": [
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  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 14
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25958108137",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/VarCon",
  "_commit": {
    "id": "b86f75b3dce88e5d10fb9c9c21a38c95075e1bd0",
    "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": 1777380870
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  "_maintainer": {
    "name": "Johannes Ptok",
    "email": "johannes.ptok@posteo.de",
    "login": "caggtaagtat",
    "uuid": 38690958
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "Biostrings",
      "role": "Depends"
    },
    {
      "package": "BSgenome",
      "role": "Depends"
    },
    {
      "package": "GenomicRanges",
      "role": "Depends"
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      "package": "methods",
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    },
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    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
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    },
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    },
    {
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    },
    {
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    },
    {
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      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
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  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.21.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.20.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "functionalgenomics",
    "alternativesplicing"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 361,
    "source": "https://www.bioconductor.org/packages/stats/bioc/VarCon"
  },
  "_searchresults": 12,
  "_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/VarCon.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "calculateHZEIperNT",
    "calculateMaxEntScanScore",
    "generateHEXplorerPlot",
    "getMaxEntInfo",
    "getSeqInfoFromVariation",
    "prepareReferenceFasta",
    "startVarConApp"
  ],
  "_datasets": [
    {
      "name": "gene2transcript",
      "title": "Small data frame specifying a transcript to certain genes for synonymous use.",
      "object": "gene2transcript",
      "class": [
        "data.frame"
      ],
      "fields": [
        "gene_name",
        "gene_ID",
        "transcript_ID"
      ],
      "rows": 1,
      "table": true,
      "tojson": true
    },
    {
      "name": "hbg",
      "title": "Donor sequences and their HBS",
      "object": "hbg",
      "class": [
        "data.frame"
      ],
      "fields": [
        "seq",
        "hbs"
      ],
      "rows": 262144,
      "table": true,
      "tojson": true
    },
    {
      "name": "hex",
      "title": "Hexamers and Z scores",
      "object": "hex",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "seq",
        "value",
        "first",
        "second",
        "first_AA",
        "second_AA",
        "AA"
      ],
      "rows": 4096,
      "table": true,
      "tojson": true
    },
    {
      "name": "referenceDnaStringSet",
      "title": "Small DNAStringset as exemplary reference genome sequence",
      "object": "referenceDnaStringSet",
      "class": [
        "DNAStringSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "transCoord",
      "title": "Small table as exemplary transcript table with exon coordinates",
      "object": "transCoord",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Gene.stable.ID",
        "Transcript.stable.ID",
        "Strand",
        "Exon.region.start..bp.",
        "Exon.region.end..bp.",
        "cDNA.coding.start",
        "cDNA.coding.end",
        "CDS.start",
        "CDS.end",
        "Exon.rank.in.transcript",
        "Exon.stable.ID",
        "Chromosome.scaffold.name"
      ],
      "rows": 5,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "calculateHZEIperNT",
      "title": "Generates table with HZEI scores per nucleotide of a sequence.",
      "topics": [
        "calculateHZEIperNT"
      ]
    },
    {
      "page": "calculateMaxEntScanScore",
      "title": "Calculate MaxEntScan score of a splice site sequence",
      "topics": [
        "calculateMaxEntScanScore"
      ]
    },
    {
      "page": "gene2transcript",
      "title": "Small data frame specifying a transcript to certain genes for synonymous use.",
      "topics": [
        "gene2transcript"
      ]
    },
    {
      "page": "generateHEXplorerPlot",
      "title": "Generates plot with HZEI values and splice site strengths from a list holding information about an SNV.",
      "topics": [
        "generateHEXplorerPlot"
      ]
    },
    {
      "page": "getMaxEntInfo",
      "title": "Generates table with MaxEntScan scores per potential SA position.",
      "topics": [
        "getMaxEntInfo"
      ]
    },
    {
      "page": "getSeqInfoFromVariation",
      "title": "Collects information about genomic context of sequence variants.",
      "topics": [
        "getSeqInfoFromVariation"
      ]
    },
    {
      "page": "hbg",
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      "topics": [
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      "title": "Hexamers and Z scores",
      "topics": [
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      ]
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      "title": "Imports Fasta file from filepath.",
      "topics": [
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      ]
    },
    {
      "page": "referenceDnaStringSet",
      "title": "Small DNAStringset as exemplary reference genome sequence",
      "topics": [
        "referenceDnaStringSet"
      ]
    },
    {
      "page": "startVarConApp",
      "title": "Start GUI of VarCon.",
      "topics": [
        "startVarConApp"
      ]
    },
    {
      "page": "transCoord",
      "title": "Small table as exemplary transcript table with exon coordinates",
      "topics": [
        "transCoord"
      ]
    }
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  "_readme": "https://github.com/bioc/VarCon/raw/HEAD/README.md",
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      "filename": "VarCon.html",
      "title": "Analysing SNVs with VarCon",
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