{
  "_id": "6a1aee471d7bb097a09f57e1",
  "Package": "MIRA",
  "Version": "1.35.0",
  "Date": "2021-11-21",
  "Title": "Methylation-Based Inference of Regulatory Activity",
  "Description": "DNA methylation contains information about the regulatory\nstate of the cell. MIRA aggregates genome-scale DNA methylation\ndata into a DNA methylation profile for a given region set with\nshared biological annotation. Using this profile, MIRA infers\nand scores the collective regulatory activity for the region\nset. MIRA facilitates regulatory analysis in situations where\nclassical regulatory assays would be difficult and allows\npublic sources of region sets to be leveraged for novel insight\ninto the regulatory state of DNA methylation datasets.",
  "Authors@R": "c(person(\"Nathan\", \"Sheffield\", role=c(\"aut\")),\nperson(\"John\", \"Lawson\", email=\"jtl2hk@virginia.edu\", role=c(\"aut\", \"cre\")),\nperson(\"Christoph\", \"Bock\", role=c(\"ctb\")))",
  "Author": "Nathan Sheffield <http://www.databio.org> [aut], Christoph Bock\n[ctb], John Lawson [aut, cre]",
  "Maintainer": "John Lawson <jtl2hk@virginia.edu>",
  "VignetteBuilder": "knitr",
  "License": "GPL-3",
  "biocViews": "ImmunoOncology, DNAMethylation, GeneRegulation,\nGenomeAnnotation, SystemsBiology, FunctionalGenomics, ChIPSeq,\nMethylSeq, Sequencing, Epigenetics, Coverage",
  "URL": "http://databio.org/mira",
  "BugReports": "https://github.com/databio/MIRA",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:46:33 UTC",
  "RemoteUrl": "https://github.com/bioc/MIRA",
  "RemoteRef": "HEAD",
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  "NeedsCompilation": "no",
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    "User": "root"
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    "email": "jtl2hk@virginia.edu",
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      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
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      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
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      "package": "ggplot2",
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      "package": "Biobase",
      "role": "Imports"
    },
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      "package": "stats",
      "role": "Imports"
    },
    {
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      "role": "Imports"
    },
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      "role": "Imports"
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      "role": "Suggests"
    },
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      "package": "rmarkdown",
      "role": "Suggests"
    },
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      "package": "AnnotationHub",
      "role": "Suggests"
    },
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      "package": "LOLA",
      "role": "Suggests"
    }
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  "_selfowned": true,
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  "_updates": [
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      "week": "2025-44",
      "n": 2
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    "immunooncology",
    "dnamethylation",
    "generegulation",
    "genomeannotation",
    "systemsbiology",
    "functionalgenomics",
    "chipseq",
    "methylseq",
    "sequencing",
    "epigenetics",
    "coverage"
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    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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  "_downloads": {
    "count": 407,
    "source": "https://www.bioconductor.org/packages/stats/bioc/MIRA"
  },
  "_mentions": 856,
  "_devurl": "https://github.com/databio/mira",
  "_searchresults": 14,
  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/MIRA.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/databio/mira",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
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    "aggregateMethyl",
    "binRegion",
    "BSBinAggregate",
    "BSreadBiSeq",
    "bsseqToDataTable",
    "calcMIRAScore",
    "plotMIRAProfiles",
    "plotMIRAScores",
    "rbindNamedList",
    "SummarizedExperimentToDataTable"
  ],
  "_datasets": [
    {
      "name": "bigBinDT1",
      "title": "DNA methylation data for the \"Applying MIRA to a Biological Question\" vignette (1st part).",
      "object": "bigBinDT1",
      "file": "bigBinDT1.RData",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "sampleName",
        "bin",
        "methylProp",
        "sumCoverage",
        "featureID"
      ],
      "rows": 252,
      "table": true,
      "tojson": true
    },
    {
      "name": "bigBinDT2",
      "title": "DNA methylation data for the \"Applying MIRA to a Biological Question\" vignette (2nd part).",
      "object": "bigBinDT2",
      "file": "bigBinDT2.RData",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "bin",
        "methylProp",
        "sumCoverage",
        "featureID",
        "sampleName"
      ],
      "rows": 1008,
      "table": true,
      "tojson": true
    },
    {
      "name": "exampleAnnoDT1",
      "title": "A data.table with annotation for a bisulfite sample.",
      "object": "exampleAnnoDT1",
      "file": "exampleAnnoDT1.RData",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "sampleName",
        "sampleType"
      ],
      "rows": 1,
      "table": true,
      "tojson": true
    },
    {
      "name": "exampleAnnoDT2",
      "title": "Annotation data for the \"Applying MIRA to a Biological Question\" vignette.",
      "object": "exampleAnnoDT2",
      "file": "exampleAnnoDT2.RData",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "sampleName",
        "sampleType"
      ],
      "rows": 24,
      "table": true,
      "tojson": true
    },
    {
      "name": "exampleBins",
      "title": "A data.table with artificial binned methylation data",
      "object": "exampleBins",
      "file": "exampleBins.RData",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "bin",
        "methylProp",
        "sumCoverage",
        "featureID",
        "sampleName",
        "sampleType"
      ],
      "rows": 22,
      "table": true,
      "tojson": true
    },
    {
      "name": "exampleBSDT",
      "title": "A data.table containing DNA methylation data.",
      "object": "exampleBSDT",
      "file": "exampleBSDT.RData",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "chr",
        "start",
        "methylCount",
        "coverage"
      ],
      "rows": 4000,
      "table": true,
      "tojson": true
    },
    {
      "name": "exampleBSseqObj",
      "title": "A small BSseq object.",
      "object": "exampleBSseqObj",
      "file": "exampleBSseqObj.RData",
      "class": [
        "BSseq"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "exampleRegionSet",
      "title": "A Granges object with Nrf1-binding regions.",
      "object": "exampleRegionSet",
      "file": "exampleRegionSet.RData",
      "class": [
        "GRanges"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "addMethPropCol",
      "title": "Add column for proportion of methylation",
      "topics": [
        "addMethPropCol"
      ]
    },
    {
      "page": "aggregateMethyl",
      "title": "Aggregate methylation data to get a summary methylation profile for each region set",
      "topics": [
        "aggregateMethyl"
      ]
    },
    {
      "page": "bigBinDT1",
      "title": "DNA methylation data for the \"Applying MIRA to a Biological Question\" vignette (1st part).",
      "topics": [
        "bigBinDT1"
      ]
    },
    {
      "page": "bigBinDT2",
      "title": "DNA methylation data for the \"Applying MIRA to a Biological Question\" vignette (2nd part).",
      "topics": [
        "bigBinDT2"
      ]
    },
    {
      "page": "binRegion",
      "title": "Divide region into similarly sized bins.",
      "topics": [
        "binRegion"
      ]
    },
    {
      "page": "BSBinAggregate",
      "title": "Bins regions and aggregates methylation data across the regions by bin",
      "topics": [
        "BSBinAggregate"
      ]
    },
    {
      "page": "BSreadBiSeq",
      "title": "Read in files from biseq meth caller",
      "topics": [
        "BSreadBiSeq"
      ]
    },
    {
      "page": "bsseqToDataTable",
      "title": "Convert a BSseq object to data.table format for MIRA.",
      "topics": [
        "bsseqToDataTable"
      ]
    },
    {
      "page": "calcMIRAScore",
      "title": "Score methylation profile based on its shape",
      "topics": [
        "calcMIRAScore"
      ]
    },
    {
      "page": "exampleAnnoDT1",
      "title": "A data.table with annotation for a bisulfite sample.",
      "topics": [
        "exampleAnnoDT1"
      ]
    },
    {
      "page": "exampleAnnoDT2",
      "title": "Annotation data for the \"Applying MIRA to a Biological Question\" vignette.",
      "topics": [
        "exampleAnnoDT2"
      ]
    },
    {
      "page": "exampleBins",
      "title": "A data.table with artificial binned methylation data",
      "topics": [
        "exampleBins"
      ]
    },
    {
      "page": "exampleBSDT",
      "title": "A data.table containing DNA methylation data.",
      "topics": [
        "exampleBSDT"
      ]
    },
    {
      "page": "exampleBSseqObj",
      "title": "A small BSseq object.",
      "topics": [
        "exampleBSseqObj"
      ]
    },
    {
      "page": "exampleRegionSet",
      "title": "A Granges object with Nrf1-binding regions.",
      "topics": [
        "exampleRegionSet"
      ]
    },
    {
      "page": "MIRA",
      "title": "Methylation-based Inference of Regulatory Activity (MIRA)",
      "topics": [
        "MIRA-package",
        "MIRA"
      ]
    },
    {
      "page": "plotMIRAProfiles",
      "title": "Plot summary methylation profile",
      "topics": [
        "plotMIRAProfiles"
      ]
    },
    {
      "page": "plotMIRAScores",
      "title": "Plot MIRA scores and compare different conditions",
      "topics": [
        "plotMIRAScores"
      ]
    },
    {
      "page": "rbindNamedList",
      "title": "Combine data.tables from a named list into one big data.table with extra column for name.",
      "topics": [
        "rbindNamedList"
      ]
    },
    {
      "page": "SummarizedExperimentToDataTable",
      "title": "Make MIRA-compatible data.tables using information from SummarizedExperiment-based classes",
      "topics": [
        "SummarizedExperimentToDataTable"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/MIRA/raw/HEAD/README.md",
  "_rundeps": [
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    "askpass",
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  "_vignettes": [
    {
      "source": "BiologicalApplication.Rmd",
      "filename": "BiologicalApplication.html",
      "title": "Applying MIRA to a Biological Question",
      "author": "John Lawson",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Biological Question",
        "Input:",
        "Package workflow",
        "Initial Run-through",
        "Choosing Appropriate Region Sizes",
        "Full MIRA Analysis",
        "Interpreting the Results",
        "General Interpretation Tips and Caveats",
        "Other Tips for Using MIRA"
      ],
      "created": "2017-04-25 16:46:25",
      "modified": "2017-10-28 21:26:40",
      "commits": 11
    },
    {
      "source": "GettingStarted.Rmd",
      "filename": "GettingStarted.html",
      "title": "Getting Started with Methylation-based Inference of Regulatory Activity",
      "author": "John Lawson",
      "engine": "knitr::rmarkdown",
      "headings": [
        "The MIRA Bioconductor package",
        "Required inputs",
        "DNA methylation data",
        "Region sets",
        "Analysis workflow",
        "The input",
        "Expand your regions",
        "Aggregating methylation across regions",
        "Calculating the MIRA score",
        "Interpreting the results",
        "Bonus: Loading region sets with LOLA"
      ],
      "created": "2017-04-25 16:46:25",
      "modified": "2019-10-24 20:11:22",
      "commits": 11
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  "_indexed": true,
  "_nocasepkg": "mira",
  "_universes": [
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