{
  "_id": "6ae76e9c1e2c7b3a4f5304f2",
  "Package": "pram",
  "Title": "Pooling RNA-seq datasets for assembling transcript models",
  "Version": "1.29.0",
  "Authors@R": "c(\nperson( given=\"Peng\",     family=\"Liu\",\nemail = \"pliu55.wisc+bioconductor@gmail.com\",\nrole = c(\"aut\", \"cre\")),\nperson( given=\"Colin N.\", family=\"Dewey\", role = c(\"aut\")),\nperson( given=\"Sündüz\",   family=\"Keleş\", role = c(\"aut\")) )",
  "Description": "Publicly available RNA-seq data is routinely used for\nretrospective analysis to elucidate new biology.  Novel\ntranscript discovery enabled by large collections of RNA-seq\ndatasets has emerged as one of such analysis.  To increase the\npower of transcript discovery from large collections of RNA-seq\ndatasets, we developed a new R package named Pooling RNA-seq\nand Assembling Models (PRAM), which builds transcript models in\nintergenic regions from pooled RNA-seq datasets.  This package\nincludes functions for defining intergenic regions, extracting\nand pooling related RNA-seq alignments, predicting, selected,\nand evaluating transcript models.",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "URL": "https://github.com/pliu55/pram",
  "BugReports": "https://github.com/pliu55/pram/issues",
  "RoxygenNote": "6.1.0",
  "Collate": "'Param.R' 'Transcript.R' 'buildModel.R' 'defIgRanges.R'\n'evalModel.R' 'prepIgBam.R' 'runPRAM.R' 'selModel.R' 'util.R'",
  "VignetteBuilder": "knitr",
  "biocViews": "Software, Technology, Sequencing, RNASeq,\nBiologicalQuestion, GenePrediction, GenomeAnnotation,\nResearchField, Transcriptomics",
  "SystemsRequirements": "buildModel() and runPRAM() functions require\nexternal software Cufflinks, StringTie, and/or TACO. For\ndetails, please see the 'Required external software' section in\nvignette's 'Building transcript models: buildModel()'.",
  "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:49:43 UTC",
  "RemoteUrl": "https://github.com/bioc/pram",
  "RemoteRef": "HEAD",
  "RemoteSha": "e06acb573ce9114023f0f6012dc671a8aa8cbd73",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-11-01 14:08:27 UTC",
    "User": "root"
  },
  "Author": "Peng Liu [aut, cre],\nColin N. Dewey [aut],\nSündüz Keleş [aut]",
  "Maintainer": "Peng Liu <pliu55.wisc+bioconductor@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "pram_1.29.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/38c60108c8c18a15cf3866d8b5a28c53a0f22c6214306507f7c676b2590183b0",
  "_filesize": 2908173,
  "_sha256": "38c60108c8c18a15cf3866d8b5a28c53a0f22c6214306507f7c676b2590183b0",
  "_expires": "2027-02-09T16:53:46.000Z",
  "_created": "2026-11-01T14:08:27.000Z",
  "_published": "2026-11-01T16:53:48.222Z",
  "_upstream": "https://github.com/bioc/pram",
  "_status": "success",
  "_maintainer": {
    "name": "Peng Liu",
    "email": "pliu55.wisc+bioconductor@gmail.com",
    "login": "pliu55",
    "description": "",
    "uuid": 8206016
  },
  "_jobs": [
    {
      "job": 124872221202,
      "time": 160,
      "config": "bioc-checks",
      "r": "4.6.2",
      "check": "WARNING",
      "artifact": "13087786251"
    },
    {
      "job": 124872221100,
      "time": 274,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "13087283852"
    },
    {
      "job": 124872221179,
      "time": 311,
      "config": "linux-release-x86_64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13086879962"
    },
    {
      "job": 124872221199,
      "time": 182,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "13092795339"
    },
    {
      "job": 124872221200,
      "time": 185,
      "config": "macos-release-arm64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13092705868"
    },
    {
      "job": 124864159817,
      "time": 220,
      "config": "source",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13085619937"
    },
    {
      "job": 124872221080,
      "time": 124,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "13086869470"
    },
    {
      "job": 124872221103,
      "time": 137,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "13086579373"
    },
    {
      "job": 124872221176,
      "time": 172,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "13085789594"
    },
    {
      "job": 124872221132,
      "time": 171,
      "config": "windows-release-x86_64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13086991229"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 4,
    "note": 6
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41310447012",
  "_commit": {
    "id": "e06acb573ce9114023f0f6012dc671a8aa8cbd73",
    "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": 1777380583
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "tools",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "version": ">= 1.11.8",
      "role": "Imports"
    },
    {
      "package": "GenomicAlignments",
      "version": ">= 1.16.0",
      "role": "Imports"
    },
    {
      "package": "rtracklayer",
      "version": ">= 1.40.6",
      "role": "Imports"
    },
    {
      "package": "BiocGenerics",
      "version": ">= 0.26.0",
      "role": "Imports"
    },
    {
      "package": "Seqinfo",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "version": ">= 1.32.0",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "version": ">= 2.14.12",
      "role": "Imports"
    },
    {
      "package": "Rsamtools",
      "version": ">= 1.32.3",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "version": ">= 0.18.3",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.29.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.28.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "software",
    "technology",
    "sequencing",
    "rnaseq",
    "biologicalquestion",
    "geneprediction",
    "genomeannotation",
    "researchfield",
    "transcriptomics",
    "bioconductor-package",
    "genome-annotation",
    "rna-seq",
    "transcript-model"
  ],
  "_stars": 2,
  "_contributors": [
    {
      "user": "pliu55",
      "count": 455,
      "uuid": 8206016
    },
    {
      "user": "nturaga",
      "count": 2,
      "uuid": 2746443
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 482,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 584,
    "source": "https://www.bioconductor.org/packages/stats/bioc/pram"
  },
  "_devurl": "https://github.com/pliu55/pram",
  "_searchresults": 3,
  "_abi": {
    "exports": [
      {
        "key": "pram::Param",
        "hash": "044c131113e0891d"
      },
      {
        "key": "pram::Transcript",
        "hash": "ba7f10d3de35d7cc"
      },
      {
        "key": "pram::generic:checkCufflinksBin",
        "hash": "44fffea4a79e7dd4"
      },
      {
        "key": "pram::generic:checkCuffmergeRequiredBins",
        "hash": "adb76663daf27cc8"
      },
      {
        "key": "pram::generic:checkStringTieBin",
        "hash": "228e0512004732bb"
      },
      {
        "key": "pram::generic:checkTacoBin",
        "hash": "05f6980a93dd44d2"
      },
      {
        "key": "pram::generic:chipseqmaxndupaln",
        "hash": "5ea1449d233dcbae"
      },
      {
        "key": "pram::generic:chromoridt",
        "hash": "f1af60062c7742c7"
      },
      {
        "key": "pram::generic:chromoridt<-",
        "hash": "9c87aeb72107e7ca"
      },
      {
        "key": "pram::generic:cufflinks",
        "hash": "dea359e999ac9fc9"
      },
      {
        "key": "pram::generic:cufflinks<-",
        "hash": "576753d9affefd8e"
      },
      {
        "key": "pram::generic:cufflinkslibtype",
        "hash": "21cab34fbb604a95"
      },
      {
        "key": "pram::generic:cufflinksreffa",
        "hash": "7cb44175c1cb3b70"
      },
      {
        "key": "pram::generic:cufflinksreffa<-",
        "hash": "c89b06bad4d4547c"
      },
      {
        "key": "pram::generic:cvnfolds",
        "hash": "88908c3106cd1470"
      },
      {
        "key": "pram::generic:cvnfolds<-",
        "hash": "fe8ba0b8334662eb"
      },
      {
        "key": "pram::generic:evalModel",
        "hash": "a994724b1d10dd02"
      },
      {
        "key": "pram::generic:exprmintpm",
        "hash": "a8943dcd6e8590dc"
      },
      {
        "key": "pram::generic:exprmintpm<-",
        "hash": "16e029c8962be238"
      },
      {
        "key": "pram::generic:foutgtf",
        "hash": "77d4e99826f1ba1e"
      },
      {
        "key": "pram::generic:foutgtf<-",
        "hash": "150bf77b7c07b132"
      },
      {
        "key": "pram::generic:fr1ststrand2mate2flag",
        "hash": "6eab900279255b0f"
      },
      {
        "key": "pram::generic:fuserbams",
        "hash": "8e3d76de0a4aa8e6"
      },
      {
        "key": "pram::generic:fuserbams<-",
        "hash": "e6983ef51e2fc6ad"
      },
      {
        "key": "pram::generic:getExon",
        "hash": "b126f7fb4a88f331"
      },
      {
        "key": "pram::generic:getIdxStatsFromBam",
        "hash": "c0ff8c8a5c055313"
      },
      {
        "key": "pram::generic:getJnc",
        "hash": "44e59309c8998cee"
      },
      {
        "key": "pram::generic:getMaxChromGRangesFromBams",
        "hash": "fea19838822f5c8c"
      },
      {
        "key": "pram::generic:getTr",
        "hash": "0e3056a3edaf60fd"
      },
      {
        "key": "pram::generic:gtfinfokeys",
        "hash": "67f70a4fc7741421"
      },
      {
        "key": "pram::generic:iggrs",
        "hash": "8bca100a4782f572"
      },
      {
        "key": "pram::generic:iggrs<-",
        "hash": "a895e9da7082dfaa"
      },
      {
        "key": "pram::generic:managerdt",
        "hash": "c6e4a0d825cc07bf"
      },
      {
        "key": "pram::generic:managerdt<-",
        "hash": "0fa15e43ff774fdc"
      },
      {
        "key": "pram::generic:maxchromlen",
        "hash": "49cbe150285b51b5"
      },
      {
        "key": "pram::generic:maxmulndupaln",
        "hash": "2033928fbd832dd3"
      },
      {
        "key": "pram::generic:maxmulndupaln<-",
        "hash": "36ced3f40b98fc22"
      },
      {
        "key": "pram::generic:maxmultireadfraction",
        "hash": "61072e38e8ac2947"
      },
      {
        "key": "pram::generic:maxunindupaln",
        "hash": "4a1a0ff76258a55d"
      },
      {
        "key": "pram::generic:maxunindupaln<-",
        "hash": "b299e8f6b7030df6"
      },
      {
        "key": "pram::generic:maxyieldsize",
        "hash": "1c4ea5d96f717738"
      },
      {
        "key": "pram::generic:minfragspertransfrag",
        "hash": "840a9edc9e52d2c5"
      },
      {
        "key": "pram::generic:minisoformfraction",
        "hash": "b2cb5d9c215b6a1f"
      },
      {
        "key": "pram::generic:mintrfpkmtoinclude",
        "hash": "bd4d70791e26069c"
      },
      {
        "key": "pram::generic:mintrtpmtoinclude",
        "hash": "6b16265c0adb0362"
      },
      {
        "key": "pram::generic:nthreads",
        "hash": "876609294204c41f"
      },
      {
        "key": "pram::generic:nthreads<-",
        "hash": "e51a733dc70adae4"
      },
      {
        "key": "pram::generic:os2cufflinks_url",
        "hash": "3a6a712f607c8444"
      },
      {
        "key": "pram::generic:os2stringtie_url",
        "hash": "61bf5bdc4617badb"
      },
      {
        "key": "pram::generic:os2taco_url",
        "hash": "d4bab8d756400163"
      },
      {
        "key": "pram::generic:randomseed",
        "hash": "51a134ffc844d393"
      },
      {
        "key": "pram::generic:stringtie",
        "hash": "7cde8635a2c81513"
      },
      {
        "key": "pram::generic:stringtie<-",
        "hash": "ed851a33aadd6308"
      },
      {
        "key": "pram::generic:stringtielibtype",
        "hash": "b3c1205aba1c0e41"
      },
      {
        "key": "pram::generic:taco",
        "hash": "d9e1ad2322095c64"
      },
      {
        "key": "pram::generic:taco<-",
        "hash": "d7e41a97a4e0c8b1"
      },
      {
        "key": "pram::generic:tmpdir",
        "hash": "61a4d01791c0d08c"
      },
      {
        "key": "pram::generic:tmpdir<-",
        "hash": "b812cd82b13df983"
      },
      {
        "key": "pram::generic:tsstesextwidth",
        "hash": "8b978b0a83d93c7e"
      }
    ],
    "imports": []
  },
  "_rbuild": "4.6.2",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/pram.html",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/pliu55/pram",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "buildModel",
    "defIgRanges",
    "evalModel",
    "prepIgBam",
    "runPRAM",
    "selModel"
  ],
  "_help": [
    {
      "page": "buildModel",
      "title": "Build transcript models from aligned RNA-seq data",
      "topics": [
        "buildModel"
      ]
    },
    {
      "page": "defIgRanges",
      "title": "Define intergenic genomic regions",
      "topics": [
        "defIgRanges"
      ]
    },
    {
      "page": "evalModel",
      "title": "Evaluate transcript model",
      "topics": [
        "evalModel",
        "evalModel,character,character-method",
        "evalModel,character,data.table-method",
        "evalModel,data.table,data.table-method",
        "evalModel,GRanges,GRanges-method"
      ]
    },
    {
      "page": "prepIgBam",
      "title": "Extract alignments in intergenic regions from BAM files",
      "topics": [
        "prepIgBam"
      ]
    },
    {
      "page": "runPRAM",
      "title": "Predict intergenic transcript models from RNA-seq",
      "topics": [
        "runPRAM"
      ]
    },
    {
      "page": "selModel",
      "title": "Select transcript models",
      "topics": [
        "selModel"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/pram/raw/HEAD/README.md",
  "_rundeps": [
    "askpass",
    "BH",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "Biostrings",
    "bitops",
    "cigarillo",
    "codetools",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicAlignments",
    "GenomicRanges",
    "httr",
    "IRanges",
    "jsonlite",
    "lambda.r",
    "mime",
    "openssl",
    "R6",
    "RCurl",
    "restfulr",
    "Rhtslib",
    "rjson",
    "Rsamtools",
    "rtracklayer",
    "S4Vectors",
    "Seqinfo",
    "snow",
    "sys",
    "XML",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "pram.Rmd",
      "filename": "pram.html",
      "title": "PRAM: Pooling RNA-seq and Assembling Models",
      "author": "Peng Liu, Colin N. Dewey, and Sündüz Keleş",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "From GitHub",
        "From Bioconductor",
        "Quick start",
        "Description",
        "Examples",
        "Define intergenic genomic ranges: defIgRanges()",
        "Example",
        "Prepare input RNA-seq alignments: prepIgBam()",
        "Build transcript models: buildModel()",
        "Transcript prediction methods",
        "Required external software",
        "Select transcript models: selModel()",
        "Evaluate transcript models: evalModel()",
        "Motivation",
        "Input",
        "Output",
        "Session Info"
      ],
      "created": "2018-05-15 14:35:53",
      "modified": "2022-10-09 13:02:44",
      "commits": 24
    }
  ],
  "_score": 4.301029995663981,
  "_indexed": true,
  "_nocasepkg": "pram",
  "_universes": [
    "bioc",
    "pliu55"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.29.0",
      "date": "2026-11-01T14:31:01.000Z",
      "distro": "resolute",
      "commit": "e06acb573ce9114023f0f6012dc671a8aa8cbd73",
      "fileid": "https://r2.ropensci.org/864abe0659645a6839d785255ff61ae5cea7bb793609287d69709ae1110c7c53",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310447012"
    },
    {
      "r": "4.6.2",
      "os": "linux",
      "version": "1.29.0",
      "date": "2026-11-01T14:31:44.000Z",
      "distro": "resolute",
      "commit": "e06acb573ce9114023f0f6012dc671a8aa8cbd73",
      "fileid": "https://r2.ropensci.org/ef9e23bca0d0b6a62b10fd0ffd63bfed007544987a86231e714b38546f5c85e3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310447012"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.29.0",
      "date": "2026-11-01T16:51:58.000Z",
      "commit": "e06acb573ce9114023f0f6012dc671a8aa8cbd73",
      "fileid": "https://r2.ropensci.org/4eeade734c5d8400d411d119db5b531bc894d47dddfd5793ceba6fcffb0ab44f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310447012"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "1.29.0",
      "date": "2026-11-01T16:52:04.000Z",
      "commit": "e06acb573ce9114023f0f6012dc671a8aa8cbd73",
      "fileid": "https://r2.ropensci.org/7ec1789aee71061630123705bc2497513c5d7cb2b661a404a596cf2a53bf1bb2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310447012"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.29.0",
      "date": "2026-11-01T14:30:06.000Z",
      "commit": "e06acb573ce9114023f0f6012dc671a8aa8cbd73",
      "fileid": "https://r2.ropensci.org/a492be912f108ee8e59df4ba9e678881cf24c9dadaf0c4cac721392e75a832a4",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310447012"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.29.0",
      "date": "2026-11-01T14:10:00.000Z",
      "commit": "e06acb573ce9114023f0f6012dc671a8aa8cbd73",
      "fileid": "https://r2.ropensci.org/584594e34abfbd673e58eb23e450b1821e40a424b98c8d01dfd615314dcb7570",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310447012"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.29.0",
      "date": "2026-11-01T14:10:09.000Z",
      "commit": "e06acb573ce9114023f0f6012dc671a8aa8cbd73",
      "fileid": "https://r2.ropensci.org/8ecb25b1f16073daf06562d174db50221a9abfeb359ca829d3c8b66b378a268d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310447012"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "1.29.0",
      "date": "2026-11-01T14:10:21.000Z",
      "commit": "e06acb573ce9114023f0f6012dc671a8aa8cbd73",
      "fileid": "https://r2.ropensci.org/23973f1511ba799a3e9ffa45253d331219aac69b44f5e76d39bca26497aa5d96",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310447012"
    }
  ]
}