{
  "_id": "6a197affacfb0bcc41df5825",
  "Package": "Wrench",
  "Type": "Package",
  "Title": "Wrench normalization for sparse count data",
  "Version": "1.31.0",
  "Authors@R": "c( person(\"Senthil Kumar\", \"Muthiah\",\nemail=\"smuthiah@umiacs.umd.edu\",\nrole = c(\"aut\")),\nperson(\"Hector\", \"Corrada Bravo\",\nemail = \"hcorrada@gmail.com\",\nrole = c(\"aut\", \"cre\"))\n)",
  "Description": "Wrench is a package for normalization sparse genomic count\ndata, like that arising from 16s metagenomic surveys.",
  "License": "Artistic-2.0",
  "RoxygenNote": "6.1.0",
  "VignetteBuilder": "knitr",
  "biocViews": "Normalization, Sequencing, Software",
  "URL": "https://github.com/HCBravoLab/Wrench",
  "BugReports": "https://github.com/HCBravoLab/Wrench/issues",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:49:02 UTC",
  "RemoteUrl": "https://github.com/bioc/Wrench",
  "RemoteRef": "HEAD",
  "RemoteSha": "977987e83fdeaa9db72e5af852f50499577b2f35",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-29 09:52:20 UTC",
    "User": "root"
  },
  "Author": "Senthil Kumar Muthiah [aut],\nHector Corrada Bravo [aut, cre]",
  "Maintainer": "Hector Corrada Bravo <hcorrada@gmail.com>",
  "MD5sum": "75e0588a8d6a7335ccecba2db1c03022",
  "_user": "bioc",
  "_type": "src",
  "_file": "Wrench_1.31.0.tar.gz",
  "_fileid": "dd06906f46d9a81081243a348e0eed1d2a643a22a4e96028fe36f9ff7b0a190d",
  "_filesize": 108700,
  "_sha256": "dd06906f46d9a81081243a348e0eed1d2a643a22a4e96028fe36f9ff7b0a190d",
  "_created": "2026-05-29T09:52:20.000Z",
  "_published": "2026-05-29T11:39:43.818Z",
  "_jobs": [
    {
      "job": 78478162510,
      "time": 161,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7287996309"
    },
    {
      "job": 78478162490,
      "time": 177,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7288001130"
    },
    {
      "job": 78478162502,
      "time": 186,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7288003489"
    },
    {
      "job": 78478162499,
      "time": 181,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7289779278"
    },
    {
      "job": 78478162514,
      "time": 117,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7289759625"
    },
    {
      "job": 78477595387,
      "time": 215,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7287947167"
    },
    {
      "job": 78478162463,
      "time": 129,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7287986368"
    },
    {
      "job": 78478162528,
      "time": 130,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7287987139"
    },
    {
      "job": 78478162504,
      "time": 116,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7287982653"
    },
    {
      "job": 78478162559,
      "time": 114,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7287982310"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 8
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26630414621",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/Wrench",
  "_commit": {
    "id": "977987e83fdeaa9db72e5af852f50499577b2f35",
    "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": 1777380542
  },
  "_maintainer": {
    "name": "Hector Corrada Bravo",
    "email": "hcorrada@gmail.com",
    "login": "hcorrada",
    "description": "",
    "uuid": 2072476
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "locfit",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "metagenomeSeq",
      "role": "Suggests"
    },
    {
      "package": "DESeq2",
      "role": "Suggests"
    },
    {
      "package": "edgeR",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 7,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.31.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.30.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "normalization",
    "sequencing",
    "software"
  ],
  "_stars": 6,
  "_contributors": [
    {
      "user": "jkanche",
      "count": 7,
      "uuid": 399324
    },
    {
      "user": "smuthiah",
      "count": 6,
      "uuid": 5341245
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "hcorrada",
      "count": 1,
      "uuid": 2072476
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 2697,
    "source": "https://www.bioconductor.org/packages/stats/bioc/Wrench"
  },
  "_mentions": 2,
  "_devurl": "https://github.com/hcbravolab/wrench",
  "_searchresults": 27,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "extra/Wrench.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/hcbravolab/wrench",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "wrench"
  ],
  "_help": [
    {
      "page": "dot-estimSummary",
      "title": "Obtain robust means. .",
      "topics": [
        ".estimSummary"
      ]
    },
    {
      "page": "dot-getCondLogWeights",
      "title": "Log Postive-conditional weight computations for wrench estimators.",
      "topics": [
        ".getCondLogWeights"
      ]
    },
    {
      "page": "dot-getCondWeights",
      "title": "Postive-conditional weight computations for wrench estimators.",
      "topics": [
        ".getCondWeights"
      ]
    },
    {
      "page": "dot-getHurdle",
      "title": "Obtains logistic fits for presence/absence and fitted probabilities of a zero occurring.",
      "topics": [
        ".getHurdle"
      ]
    },
    {
      "page": "dot-getMargWeights",
      "title": "Marginal weight computations for wrench estimators.",
      "topics": [
        ".getMargWeights"
      ]
    },
    {
      "page": "dot-getReference",
      "title": "This function generates the reference.",
      "topics": [
        ".getReference"
      ]
    },
    {
      "page": "dot-gets2",
      "title": "Obtain variances of logged counts.",
      "topics": [
        ".gets2"
      ]
    },
    {
      "page": "dot-getWeightedMean",
      "title": "Get weighted means for matrix",
      "topics": [
        ".getWeightedMean"
      ]
    },
    {
      "page": "dot-getWeightedMedian",
      "title": "Get weighted median for matrix",
      "topics": [
        ".getWeightedMedian"
      ]
    },
    {
      "page": "wrench",
      "title": "Normalization for sparse, under-sampled count data.",
      "topics": [
        "wrench"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/Wrench/raw/HEAD/README.md",
  "_rundeps": [
    "lattice",
    "limma",
    "locfit",
    "matrixStats",
    "statmod"
  ],
  "_vignettes": [
    {
      "source": "vignette.Rmd",
      "filename": "vignette.html",
      "title": "Wrench",
      "author": "M. Senthil Kumar$^1$, Héctor Corrada Bravo$^1$, $^1$Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20740.",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Abstract",
        "Introduction",
        "Installation",
        "Running Wrench",
        "Usage with differential abundance pipelines",
        "Some caveats / work in development",
        "The \"detrend\" option",
        "Session Info"
      ],
      "created": "2018-10-05 17:33:55",
      "modified": "2018-10-23 15:38:14",
      "commits": 6
    }
  ],
  "_score": 7.7407665061130855,
  "_indexed": true,
  "_nocasepkg": "wrench",
  "_universes": [
    "bioc",
    "hcorrada",
    "hcbravolab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.31.0",
      "date": "2026-05-29T09:55:02.000Z",
      "distro": "noble",
      "commit": "977987e83fdeaa9db72e5af852f50499577b2f35",
      "fileid": "dbe48c6c554e1917a171e33a8f233e98ebac352ca40e47d3eae857f3bb04d6ed",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26630414621"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.31.0",
      "date": "2026-05-29T09:55:09.000Z",
      "distro": "noble",
      "commit": "977987e83fdeaa9db72e5af852f50499577b2f35",
      "fileid": "28ec9fb465cdf7fa0c547ec440ad39f9d870235f8232388542bce739796abbca",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26630414621"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.31.0",
      "date": "2026-05-29T11:39:02.000Z",
      "commit": "977987e83fdeaa9db72e5af852f50499577b2f35",
      "fileid": "29661248dba6b884a897dcba2b12ceb4a297180f5f359766b7c52ceeb480c405",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26630414621"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.31.0",
      "date": "2026-05-29T11:37:51.000Z",
      "commit": "977987e83fdeaa9db72e5af852f50499577b2f35",
      "fileid": "167923c2cff55ecd32d35663705ecdb52cdad4148ca981d1f7aa0ddd909cd29c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26630414621"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.31.0",
      "date": "2026-05-29T09:54:44.000Z",
      "commit": "977987e83fdeaa9db72e5af852f50499577b2f35",
      "fileid": "1adb094d915af207fbfbd359410c5b9214b28309bc8adffd6c4e6d6b42fc885c",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26630414621"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-05-29T09:54:09.000Z",
      "commit": "977987e83fdeaa9db72e5af852f50499577b2f35",
      "fileid": "6c0d959cd5712e0a07bb09581a4321cac2c0198f900f8e2f03e816828b1dbfaa",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26630414621"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-05-29T09:53:56.000Z",
      "commit": "977987e83fdeaa9db72e5af852f50499577b2f35",
      "fileid": "410a47559b480687234775e6855ca22f5f340da6d08b65044ff50826c894e8fd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26630414621"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.31.0",
      "date": "2026-05-29T09:53:55.000Z",
      "commit": "977987e83fdeaa9db72e5af852f50499577b2f35",
      "fileid": "2a8616603656cf1ed9e5e2eef8dbdd0e81a408096bee1cbce9f2bf8a25b675ea",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26630414621"
    }
  ]
}