{
  "_id": "6ae523ab95ca2370cc8d08bd",
  "Package": "mpra",
  "Version": "1.35.0",
  "Title": "Analyze massively parallel reporter assays",
  "Description": "Tools for data management, count preprocessing, and\ndifferential analysis in massively parallel report assays\n(MPRA).",
  "Authors@R": "c(\nperson(\"Leslie\", \"Myint\", role = c(\"cre\", \"aut\"), email = \"leslie.myint@gmail.com\"),\nperson(c(\"Kasper\", \"D.\"), \"Hansen\", role = \"aut\"))",
  "Collate": "mpra_set.R utils.R fit.R",
  "VignetteBuilder": "knitr",
  "License": "Artistic-2.0",
  "URL": "https://github.com/hansenlab/mpra",
  "BugReports": "https://github.com/hansenlab/mpra/issues",
  "biocViews": "Software, GeneRegulation, Sequencing, FunctionalGenomics",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:46:52 UTC",
  "RemoteUrl": "https://github.com/bioc/mpra",
  "RemoteRef": "HEAD",
  "RemoteSha": "8dee10e44d43cbc3136dc7b0821f32ee91bd298d",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-30 21:45:08 UTC",
    "User": "root"
  },
  "Author": "Leslie Myint [cre, aut],\nKasper D. Hansen [aut]",
  "Maintainer": "Leslie Myint <leslie.myint@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "mpra_1.35.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/8ff34964e7b24c4321299f5ee343b83d33a32d7866949d388f76d5b336c869b6",
  "_filesize": 3120313,
  "_sha256": "8ff34964e7b24c4321299f5ee343b83d33a32d7866949d388f76d5b336c869b6",
  "_expires": "2027-02-07T23:09:29.000Z",
  "_created": "2026-10-30T21:45:08.000Z",
  "_published": "2026-10-30T23:09:31.529Z",
  "_upstream": "https://github.com/bioc/mpra",
  "_status": "success",
  "_maintainer": {
    "name": "Leslie Myint",
    "email": "leslie.myint@gmail.com",
    "login": "lmyint",
    "twitter": "@lesliemyint",
    "description": "",
    "uuid": 5376916
  },
  "_jobs": [
    {
      "job": 124329806179,
      "time": 157,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "13014272975"
    },
    {
      "job": 124329806227,
      "time": 329,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "13014278358"
    },
    {
      "job": 124329806423,
      "time": 286,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "13015026354"
    },
    {
      "job": 124329806338,
      "time": 214,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "13018996681"
    },
    {
      "job": 124329806251,
      "time": 210,
      "config": "macos-release-arm64",
      "r": "4.6.2",
      "check": "NOTE",
      "artifact": "13019496747"
    },
    {
      "job": 124325220757,
      "time": 220,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "13013593820"
    },
    {
      "job": 124329806268,
      "time": 104,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "13014487024"
    },
    {
      "job": 124329806296,
      "time": 170,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "13014277804"
    },
    {
      "job": 124329806321,
      "time": 206,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "13015965167"
    },
    {
      "job": 124329806559,
      "time": 190,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "13015750240"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 6
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41130889447",
  "_commit": {
    "id": "8dee10e44d43cbc3136dc7b0821f32ee91bd298d",
    "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": 1777380412
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "BiocGenerics",
      "role": "Depends"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Depends"
    },
    {
      "package": "limma",
      "role": "Depends"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "statmod",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.35.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.34.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "software",
    "generegulation",
    "sequencing",
    "functionalgenomics"
  ],
  "_stars": 6,
  "_contributors": [
    {
      "user": "lmyint",
      "count": 51,
      "uuid": 5376916
    },
    {
      "user": "kasperdanielhansen",
      "count": 30,
      "uuid": 4956575
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "jwokaty",
      "count": 8,
      "uuid": 1744257
    },
    {
      "user": "mikelove",
      "count": 6,
      "uuid": 69203
    },
    {
      "user": "hpages",
      "count": 3,
      "uuid": 8810451
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "pi-zz-a",
      "count": 1,
      "uuid": 33691024
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 480,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 700,
    "source": "https://www.bioconductor.org/packages/stats/bioc/mpra"
  },
  "_mentions": 2,
  "_devurl": "https://github.com/hansenlab/mpra",
  "_searchresults": 35,
  "_abi": {
    "exports": [
      {
        "key": "mpra::MPRASet",
        "hash": "5aca3e5896ecee62"
      }
    ],
    "imports": [
      {
        "key": "S4Vectors::Annotated",
        "hash": "9b5b8ee6ad9969f8"
      },
      {
        "key": "S4Vectors::RectangularData",
        "hash": "d414a10823a4aada"
      },
      {
        "key": "S4Vectors::Vector",
        "hash": "09cab0bd77ae353b"
      },
      {
        "key": "S4Vectors::vector_OR_Vector",
        "hash": "f3fc18c9f8ff2633"
      },
      {
        "key": "SummarizedExperiment::SummarizedExperiment",
        "hash": "d53ca73257d1e8cf"
      }
    ]
  },
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/mpra.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/hansenlab/mpra",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "compute_logratio",
    "get_precision_weights",
    "getBarcode",
    "getDNA",
    "getEid",
    "getEseq",
    "getRNA",
    "mpralm",
    "MPRASet",
    "normalize_counts",
    "show"
  ],
  "_datasets": [
    {
      "name": "mpraSetAggExample",
      "title": "Example data for the mpra package.",
      "object": "mpraSetAggExample",
      "file": "mpraSetAggExample.rda",
      "class": [
        "MPRASet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "mpraSetAllelicExample",
      "title": "Example data for the mpra package.",
      "object": "mpraSetAllelicExample",
      "file": "mpraSetAllelicExample.rda",
      "class": [
        "MPRASet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "mpraSetExample",
      "title": "Example data for the mpra package.",
      "object": "mpraSetExample",
      "file": "mpraSetExample.rda",
      "class": [
        "MPRASet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "mpra-package",
      "title": "Analyze massively parallel reporter assays",
      "topics": [
        "mpra-package",
        "mpra"
      ]
    },
    {
      "page": "compute_logratio",
      "title": "Compute activity measure (log-ratio) for each element.",
      "topics": [
        "compute_logratio"
      ]
    },
    {
      "page": "get_precision_weights",
      "title": "Get precision weights from the copy number-variance relationship.",
      "topics": [
        "get_precision_weights"
      ]
    },
    {
      "page": "mpralm",
      "title": "Linear models for differential analysis of MPRA data",
      "topics": [
        "mpralm"
      ]
    },
    {
      "page": "MPRASet-class",
      "title": "Class '\"MPRASet\"'",
      "topics": [
        "getBarcode",
        "getDNA",
        "getEid",
        "getEseq",
        "getRNA",
        "MPRASet",
        "MPRASet-class",
        "show,MPRASet-method"
      ]
    },
    {
      "page": "mpraSetExample",
      "title": "Example data for the mpra package.",
      "topics": [
        "mpraSetAggExample",
        "mpraSetAllelicExample",
        "mpraSetExample"
      ]
    },
    {
      "page": "normalize_counts",
      "title": "Total count normalization of DNA and RNA counts",
      "topics": [
        "normalize_counts"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/mpra/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "Biobase",
    "BiocGenerics",
    "cli",
    "DelayedArray",
    "farver",
    "generics",
    "GenomicRanges",
    "glue",
    "IRanges",
    "labeling",
    "lattice",
    "lifecycle",
    "limma",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "R6",
    "RColorBrewer",
    "rlang",
    "S4Arrays",
    "S4Vectors",
    "scales",
    "Seqinfo",
    "SparseArray",
    "statmod",
    "SummarizedExperiment",
    "viridisLite",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "mpra.Rmd",
      "filename": "mpra.html",
      "title": "The mpra User's Guide",
      "author": "Leslie Myint, Kasper Daniel Hansen",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "How to cite",
        "Dependencies",
        "Creating an MPRASet object",
        "Tissue comparison",
        "Allele comparison",
        "Analysis",
        "Allelic comparison",
        "Returning an MPRASet",
        "Session Info",
        "References"
      ],
      "created": "2017-08-26 00:33:40",
      "modified": "2024-09-13 21:48:09",
      "commits": 12
    }
  ],
  "_score": 6.468347330412158,
  "_indexed": true,
  "_nocasepkg": "mpra",
  "_universes": [
    "bioc",
    "lmyint",
    "hansenlab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.35.0",
      "date": "2026-10-30T21:52:05.000Z",
      "distro": "resolute",
      "commit": "8dee10e44d43cbc3136dc7b0821f32ee91bd298d",
      "fileid": "https://r2.ropensci.org/3d5b3600fc42cc90cfbd63a15003ef5fd5a990f2672eebbb1eef0bb4826359a3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41130889447"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.35.0",
      "date": "2026-10-30T21:51:43.000Z",
      "distro": "resolute",
      "commit": "8dee10e44d43cbc3136dc7b0821f32ee91bd298d",
      "fileid": "https://r2.ropensci.org/eed184b271b50d0556ac9a2cf2204c6af808940cb9ed9a91a4c94f835ff9eddc",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41130889447"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.35.0",
      "date": "2026-10-30T23:07:24.000Z",
      "commit": "8dee10e44d43cbc3136dc7b0821f32ee91bd298d",
      "fileid": "https://r2.ropensci.org/e73de37192b85ea6fbb6f263354eb8dbf281d5df5c305fc43165ea4e2ef77688",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41130889447"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "1.35.0",
      "date": "2026-10-30T23:07:11.000Z",
      "commit": "8dee10e44d43cbc3136dc7b0821f32ee91bd298d",
      "fileid": "https://r2.ropensci.org/efa7bd5b37cedeb5c04b646f48837aaf593f96beaf44d8764a579d6c4a62bd55",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41130889447"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.35.0",
      "date": "2026-10-30T21:50:35.000Z",
      "commit": "8dee10e44d43cbc3136dc7b0821f32ee91bd298d",
      "fileid": "https://r2.ropensci.org/ee48ffc9ef26f6cc8f630d8dfb4d631a2886fdc898401271ed434b0891fc7be2",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41130889447"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.35.0",
      "date": "2026-10-30T21:49:03.000Z",
      "commit": "8dee10e44d43cbc3136dc7b0821f32ee91bd298d",
      "fileid": "https://r2.ropensci.org/b7c0176adebebbfae8c71423565bdc1ddb61ff1c2875c57bcdbd8ecb09282573",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41130889447"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.35.0",
      "date": "2026-10-30T21:49:07.000Z",
      "commit": "8dee10e44d43cbc3136dc7b0821f32ee91bd298d",
      "fileid": "https://r2.ropensci.org/9b8c98d6851258a9a488f9e321a580fea8a854160ca92489249d48de9409096c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41130889447"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.35.0",
      "date": "2026-10-30T21:49:09.000Z",
      "commit": "8dee10e44d43cbc3136dc7b0821f32ee91bd298d",
      "fileid": "https://r2.ropensci.org/7f377873a8ae0194d1efa2eec04f787e62b464775bc0d382d87a7fe42fbcfc7b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41130889447"
    }
  ]
}