{
  "_id": "6a4de930d253724d3f6ddfc5",
  "Package": "zFPKM",
  "Title": "A suite of functions to facilitate zFPKM transformations",
  "Version": "1.35.0",
  "Authors@R": "c( person(\"Ron\", \"Ammar\", role = c(\"aut\", \"cre\"), email =\n\"ron.ammar@bms.com\"), person(\"John\", \"Thompson\", role = \"aut\",\nemail = \"john.thompson@bms.com\") )",
  "Description": "Perform the zFPKM transform on RNA-seq FPKM data. This\nalgorithm is based on the publication by Hart et al., 2013\n(Pubmed ID 24215113). Reference recommends using zFPKM > -3 to\nselect expressed genes. Validated with encode open/closed\nchromosome data. Works well for gene level data using FPKM or\nTPM. Does not appear to calibrate well for transcript level\ndata.",
  "License": "GPL-3 | file LICENSE",
  "URL": "https://github.com/ronammar/zFPKM/",
  "BugReports": "https://github.com/ronammar/zFPKM/issues",
  "VignetteBuilder": "knitr",
  "biocViews": "ImmunoOncology, RNASeq, FeatureExtraction, Software,\nGeneExpression",
  "RoxygenNote": "6.0.1",
  "Config/pak/sysreqs": "libicu-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:46:10 UTC",
  "RemoteUrl": "https://github.com/bioc/zFPKM",
  "RemoteRef": "HEAD",
  "RemoteSha": "237460f7f7c1f51619590a58fbccb455efdae3d0",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-08 06:02:03 UTC",
    "User": "root"
  },
  "Author": "Ron Ammar [aut, cre],\nJohn Thompson [aut]",
  "Maintainer": "Ron Ammar <ron.ammar@bms.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "zFPKM_1.35.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/dcb9e3b2456c16109312980ba757f389e3a9e5696c9173564f6d386d2bbdd156",
  "_filesize": 379541,
  "_sha256": "dcb9e3b2456c16109312980ba757f389e3a9e5696c9173564f6d386d2bbdd156",
  "_expires": "2026-10-16T06:07:42.000Z",
  "_created": "2026-07-08T06:02:03.000Z",
  "_published": "2026-07-08T06:07:44.348Z",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 7
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28921048301",
  "_status": "success",
  "_upstream": "https://github.com/bioc/zFPKM",
  "_commit": {
    "id": "237460f7f7c1f51619590a58fbccb455efdae3d0",
    "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": 1777380370
  },
  "_maintainer": {
    "name": "Ron Ammar",
    "email": "ron.ammar@bms.com"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85798782544,
      "time": 182,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8159585754"
    },
    {
      "job": 85798782604,
      "time": 287,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8159615646"
    },
    {
      "job": 85798782584,
      "time": 285,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8159615157"
    },
    {
      "job": 85798782585,
      "time": 222,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8159597020"
    },
    {
      "job": 85798782573,
      "time": 218,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8159595687"
    },
    {
      "job": 85798193905,
      "time": 249,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8159534151"
    },
    {
      "job": 85798782578,
      "time": 140,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8159573702"
    },
    {
      "job": 85798782624,
      "time": 198,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8159590528"
    },
    {
      "job": 85798782627,
      "time": 195,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8159589386"
    },
    {
      "job": 85798782602,
      "time": 218,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8159595877"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.4.0",
      "role": "Depends"
    },
    {
      "package": "checkmate",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "limma",
      "role": "Suggests"
    },
    {
      "package": "edgeR",
      "role": "Suggests"
    },
    {
      "package": "GEOquery",
      "role": "Suggests"
    },
    {
      "package": "stringr",
      "role": "Suggests"
    },
    {
      "package": "printr",
      "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": "1.35.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.34.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "immunooncology",
    "rnaseq",
    "featureextraction",
    "software",
    "geneexpression"
  ],
  "_stars": 9,
  "_contributors": [
    {
      "user": "lotharukpongjs",
      "count": 9,
      "uuid": 80110649
    },
    {
      "user": "ronammar",
      "count": 8,
      "uuid": 5419280
    },
    {
      "user": "thompj27",
      "count": 2,
      "uuid": 14353770
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 469,
    "source": "https://www.bioconductor.org/packages/stats/bioc/zFPKM"
  },
  "_mentions": 3,
  "_devurl": "https://github.com/ronammar/zfpkm",
  "_searchresults": 28,
  "_rbuild": "4.6.1",
  "_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/zFPKM.html",
    "LICENSE",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/ronammar/zfpkm",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "zFPKM",
    "zFPKMPlot"
  ],
  "_help": [
    {
      "page": "zFPKM",
      "title": "zFPKM Transformation",
      "topics": [
        "zFPKM"
      ]
    },
    {
      "page": "zFPKMPlot",
      "title": "zFPKM Transformation",
      "topics": [
        "zFPKMPlot"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/zFPKM/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "backports",
    "Biobase",
    "BiocGenerics",
    "checkmate",
    "cli",
    "cpp11",
    "DelayedArray",
    "dplyr",
    "farver",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "IRanges",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "RColorBrewer",
    "rlang",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "zFPKM.Rmd",
      "filename": "zFPKM.html",
      "title": "Introduction to zFPKM Transformation",
      "author": "Ron Ammar",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Summary",
        "Identifying active genes for subsequent analysis",
        "References"
      ],
      "created": "2017-08-07 13:45:33",
      "modified": "2017-08-07 13:45:33",
      "commits": 1
    }
  ],
  "_score": 6.179551791165188,
  "_indexed": true,
  "_nocasepkg": "zfpkm",
  "_universes": [
    "bioc",
    "ronammar"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.35.0",
      "date": "2026-07-08T06:05:22.000Z",
      "distro": "resolute",
      "commit": "237460f7f7c1f51619590a58fbccb455efdae3d0",
      "fileid": "https://r2.ropensci.org/51b5c0a107f96ee5975d9f1c7e65344365418e4919edb73888d57245facd09f2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28921048301"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.35.0",
      "date": "2026-07-08T06:05:10.000Z",
      "distro": "resolute",
      "commit": "237460f7f7c1f51619590a58fbccb455efdae3d0",
      "fileid": "https://r2.ropensci.org/1fb6521764d1ddc6a35b23baa1d560c6cc7a072efd875c492825d255b8c4d369",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28921048301"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.35.0",
      "date": "2026-07-08T06:05:07.000Z",
      "commit": "237460f7f7c1f51619590a58fbccb455efdae3d0",
      "fileid": "https://r2.ropensci.org/11325b2274772ff7f928056ab91975547812a6de1730b3103ee2be7dfb720f62",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28921048301"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.35.0",
      "date": "2026-07-08T06:04:24.000Z",
      "commit": "237460f7f7c1f51619590a58fbccb455efdae3d0",
      "fileid": "https://r2.ropensci.org/e0640a1555edbeb161635cfcd1a5903fd21171e7cfd389cb2b75787876a79906",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28921048301"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.35.0",
      "date": "2026-07-08T06:04:53.000Z",
      "commit": "237460f7f7c1f51619590a58fbccb455efdae3d0",
      "fileid": "https://r2.ropensci.org/2081487bef1a059712fbfbfc3497bb8b195b7f56e08b99187ca82c658a1d1fb6",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28921048301"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.35.0",
      "date": "2026-07-08T06:03:45.000Z",
      "commit": "237460f7f7c1f51619590a58fbccb455efdae3d0",
      "fileid": "https://r2.ropensci.org/89a2a2e34a6716a1a7e37f736feaa0f11bbc13728c5256793bcb7da1537ecae5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28921048301"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.35.0",
      "date": "2026-07-08T06:03:54.000Z",
      "commit": "237460f7f7c1f51619590a58fbccb455efdae3d0",
      "fileid": "https://r2.ropensci.org/dff9a7d8ce91fed489eae37efbb64c1082f0770f5133a3d8768de4ecaf40cc9a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28921048301"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.35.0",
      "date": "2026-07-08T06:03:59.000Z",
      "commit": "237460f7f7c1f51619590a58fbccb455efdae3d0",
      "fileid": "https://r2.ropensci.org/4fbce0aa159200f7eb2b2e5d0e439c0cb6b08804f3fbc67ed66ae592912cab3f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28921048301"
    }
  ]
}