{
  "_id": "6a193b94acfb0bcc41dd45bf",
  "Package": "Mfuzz",
  "Version": "2.72.0",
  "Date": "2022-07-13",
  "Title": "Soft clustering of omics time series data",
  "Author": "Matthias Futschik <matthias.futschik@sysbiolab.eu>",
  "Maintainer": "Matthias Futschik <matthias.futschik@sysbiolab.eu>",
  "Description": "The Mfuzz package implements noise-robust soft clustering\nof omics time-series data, including transcriptomic, proteomic\nor metabolomic data. It is based on the use of c-means\nclustering. For convenience, it includes a graphical user\ninterface.",
  "biocViews": "Microarray, Clustering, TimeCourse, Preprocessing,\nVisualization",
  "License": "GPL-2",
  "URL": "http://mfuzz.sysbiolab.eu/",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:31:36 UTC",
  "RemoteUrl": "https://github.com/bioc/Mfuzz",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "8d3540e6fa9bf775a2c8d9247c475836e768bcd8",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-29 06:27:55 UTC",
    "User": "root"
  },
  "MD5sum": "0992a05793822bb8535186090cf28e59",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "Mfuzz_2.72.0.tar.gz",
  "_fileid": "14463dce4b5ca301499bb4625487d74a81285cee9802cae3d4963c0f950c66b3",
  "_filesize": 849039,
  "_sha256": "14463dce4b5ca301499bb4625487d74a81285cee9802cae3d4963c0f950c66b3",
  "_created": "2026-05-29T06:27:55.000Z",
  "_published": "2026-05-29T07:09:08.803Z",
  "_jobs": [
    {
      "job": 78449686896,
      "time": 138,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7284527995"
    },
    {
      "job": 78449686884,
      "time": 138,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7284528026"
    },
    {
      "job": 78449686910,
      "time": 167,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7284534996"
    },
    {
      "job": 78449686897,
      "time": 100,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7284948081"
    },
    {
      "job": 78449686913,
      "time": 112,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7285071327"
    },
    {
      "job": 78449319202,
      "time": 185,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7284495889"
    },
    {
      "job": 78449686869,
      "time": 97,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7284518884"
    },
    {
      "job": 78449686889,
      "time": 82,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7284515266"
    },
    {
      "job": 78449686912,
      "time": 76,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7284513635"
    },
    {
      "job": 78449686916,
      "time": 82,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7284515360"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 7,
    "note": 15
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621800742",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/Mfuzz",
  "_commit": {
    "id": "8d3540e6fa9bf775a2c8d9247c475836e768bcd8",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777379496
  },
  "_maintainer": {
    "name": "Matthias Futschik",
    "email": "matthias.futschik@sysbiolab.eu"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.5.0",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "version": ">= 2.5.5",
      "role": "Depends"
    },
    {
      "package": "e1071",
      "role": "Depends"
    },
    {
      "package": "tcltk",
      "role": "Imports"
    },
    {
      "package": "tkWidgets",
      "role": "Imports"
    },
    {
      "package": "marray",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 3,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.73.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "2.72.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "microarray",
    "clustering",
    "timecourse",
    "preprocessing",
    "visualization"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 2212,
    "source": "https://www.bioconductor.org/packages/stats/bioc/Mfuzz"
  },
  "_mentions": 160,
  "_searchresults": 478,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/Mfuzz.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "acore",
    "cselection",
    "Dmin",
    "fill.NA",
    "filter.NA",
    "filter.std",
    "kmeans2",
    "kmeans2.plot",
    "membership",
    "mestimate",
    "mfuzz",
    "mfuzz.plot",
    "mfuzz.plot2",
    "mfuzzColorBar",
    "Mfuzzgui",
    "overlap",
    "overlap.plot",
    "partcoef",
    "randomise",
    "standardise",
    "standardise2",
    "table2eset",
    "top.count"
  ],
  "_datasets": [
    {
      "name": "yeast",
      "title": "Gene expression data of the yeast cell cycle",
      "object": "yeast",
      "file": "yeast.rda",
      "class": [
        "ExpressionSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "yeast.table",
      "title": "Gene expression data of the yeast cell cycle as table",
      "object": "yeast.table",
      "file": "yeast.table.txt.gz",
      "class": [
        "data.frame"
      ],
      "fields": [
        "GENE.ID",
        "cdc28_0",
        "cdc28_10",
        "cdc28_20",
        "cdc28_30",
        "cdc28_40",
        "cdc28_50",
        "cdc28_60",
        "cdc28_70",
        "cdc28_80",
        "cdc28_90",
        "cdc28_100",
        "cdc28_110",
        "cdc28_120",
        "cdc28_130",
        "cdc28_140",
        "cdc28_150",
        "cdc28_160"
      ],
      "rows": 2952,
      "table": true,
      "tojson": true
    },
    {
      "name": "yeast.table2",
      "title": "Gene expression data of the yeast cell cycle as table",
      "object": "yeast.table2",
      "file": "yeast.table2.txt.gz",
      "class": [
        "data.frame"
      ],
      "fields": [
        "GENE.ID",
        "GENE.NAME",
        "cdc28_0",
        "cdc28_10",
        "cdc28_20",
        "cdc28_30",
        "cdc28_40",
        "cdc28_50",
        "cdc28_60",
        "cdc28_70",
        "cdc28_80",
        "cdc28_90",
        "cdc28_100",
        "cdc28_110",
        "cdc28_120",
        "cdc28_130",
        "cdc28_140",
        "cdc28_150",
        "cdc28_160"
      ],
      "rows": 2951,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "acore",
      "title": "Extraction of alpha cores for soft clusters",
      "topics": [
        "acore"
      ]
    },
    {
      "page": "cselection",
      "title": "Repeated soft clustering for detection of empty clusters for estimation of optimised number of clusters",
      "topics": [
        "cselection"
      ]
    },
    {
      "page": "Dmin",
      "title": "Calculation of minimum centroid distance for a range of cluster numbers for estimation of optimised number of clusters",
      "topics": [
        "Dmin"
      ]
    },
    {
      "page": "fill.NA",
      "title": "Replacement of missing values",
      "topics": [
        "fill.NA"
      ]
    },
    {
      "page": "filter.NA",
      "title": "Filtering of genes based on number of non-available expression values.",
      "topics": [
        "filter.NA"
      ]
    },
    {
      "page": "filter.std",
      "title": "Filtering of genes based on their standard deviation.",
      "topics": [
        "filter.std"
      ]
    },
    {
      "page": "kmeans2",
      "title": "K-means clustering for gene expression data",
      "topics": [
        "kmeans2"
      ]
    },
    {
      "page": "kmeans2.plot",
      "title": "Plotting results for k-means clustering",
      "topics": [
        "kmeans2.plot"
      ]
    },
    {
      "page": "membership",
      "title": "Calculating of membership values for new data based on existing clustering",
      "topics": [
        "membership"
      ]
    },
    {
      "page": "mestimate",
      "title": "Estimate for optimal fuzzifier m",
      "topics": [
        "mestimate"
      ]
    },
    {
      "page": "mfuzz",
      "title": "Function for soft clustering based on fuzzy c-means.",
      "topics": [
        "mfuzz"
      ]
    },
    {
      "page": "mfuzz.plot",
      "title": "Plotting results for soft clustering",
      "topics": [
        "mfuzz.plot"
      ]
    },
    {
      "page": "mfuzz.plot2",
      "title": "Plotting results for soft clustering with additional options",
      "topics": [
        "mfuzz.plot2"
      ]
    },
    {
      "page": "mfuzzColorBar",
      "title": "Plots a colour bar",
      "topics": [
        "mfuzzColorBar"
      ]
    },
    {
      "page": "Mfuzzgui",
      "title": "Graphical user interface for Mfuzz package",
      "topics": [
        "Mfuzzgui"
      ]
    },
    {
      "page": "overlap",
      "title": "Calculation of the overlap of soft clusters",
      "topics": [
        "overlap"
      ]
    },
    {
      "page": "overlap.plot",
      "title": "Visualisation of cluster overlap and global clustering structure",
      "topics": [
        "overlap.plot"
      ]
    },
    {
      "page": "partcoef",
      "title": "Calculation of the partition coefficient matrix for soft clustering",
      "topics": [
        "partcoef"
      ]
    },
    {
      "page": "randomise",
      "title": "Randomisation of data",
      "topics": [
        "randomise"
      ]
    },
    {
      "page": "standardise",
      "title": "Standardization of expression data for clustering.",
      "topics": [
        "standardise"
      ]
    },
    {
      "page": "standardise2",
      "title": "Standardization in regards to selected time-point",
      "topics": [
        "standardise2"
      ]
    },
    {
      "page": "table2eset",
      "title": "Conversion of table to Expression set object.",
      "topics": [
        "table2eset"
      ]
    },
    {
      "page": "top.count",
      "title": "Determines the number for which each gene has highest membership value in all cluster",
      "topics": [
        "top.count"
      ]
    },
    {
      "page": "yeast",
      "title": "Gene expression data of the yeast cell cycle",
      "topics": [
        "yeast"
      ]
    },
    {
      "page": "yeast.table",
      "title": "Gene expression data of the yeast cell cycle as table",
      "topics": [
        "yeast.table"
      ]
    },
    {
      "page": "yeast.table2",
      "title": "Gene expression data of the yeast cell cycle as table",
      "topics": [
        "yeast.table2"
      ]
    }
  ],
  "_rundeps": [
    "Biobase",
    "BiocGenerics",
    "class",
    "DynDoc",
    "e1071",
    "generics",
    "MASS",
    "proxy",
    "tkWidgets",
    "widgetTools"
  ],
  "_vignettes": [
    {
      "source": "Mfuzz.Rnw",
      "filename": "Mfuzz.pdf",
      "title": "Introduction to Mfuzz",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2013-11-01 19:56:16",
      "modified": "2022-05-26 06:58:00",
      "commits": 6
    }
  ],
  "_score": 7.279485524348085,
  "_indexed": false,
  "_nocasepkg": "mfuzz",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/Mfuzz",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.72.0",
      "date": "2026-05-29T06:30:08.000Z",
      "distro": "noble",
      "commit": "8d3540e6fa9bf775a2c8d9247c475836e768bcd8",
      "fileid": "fd681e3e5344c46fae2217528bc822a61673243c93aa6951737fa184423b4b86",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621800742"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.72.0",
      "date": "2026-05-29T06:30:35.000Z",
      "distro": "noble",
      "commit": "8d3540e6fa9bf775a2c8d9247c475836e768bcd8",
      "fileid": "731a1c80cb3b427d1c2f36ab27006f1ac3e808ff000389f7874985a401507a54",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621800742"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.72.0",
      "date": "2026-05-29T07:00:11.000Z",
      "commit": "8d3540e6fa9bf775a2c8d9247c475836e768bcd8",
      "fileid": "a90089b9df90deee81edefc932e5550257d9827e359343e74f32c56d97bb9591",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621800742"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.72.0",
      "date": "2026-05-29T07:08:24.000Z",
      "commit": "8d3540e6fa9bf775a2c8d9247c475836e768bcd8",
      "fileid": "ad0730307df98293e23c3e0ff5dc2eccbaf70ca2a0a12d62ef21ddedefe9ab2a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621800742"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.72.0",
      "date": "2026-05-29T06:29:52.000Z",
      "commit": "8d3540e6fa9bf775a2c8d9247c475836e768bcd8",
      "fileid": "078ea61176b3976b12e82bb2e8f3d265bc17df8ebcf4a13cc5e7b2f47d0e2217",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621800742"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.72.0",
      "date": "2026-05-29T06:29:05.000Z",
      "commit": "8d3540e6fa9bf775a2c8d9247c475836e768bcd8",
      "fileid": "ba75f5378462d9b54ba112eabf08ca90209e58e3aab193b901a5436bf14f846f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621800742"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.72.0",
      "date": "2026-05-29T06:29:03.000Z",
      "commit": "8d3540e6fa9bf775a2c8d9247c475836e768bcd8",
      "fileid": "bc6b72d6a188d58c16399fe5c570a7ce20acda6a985024f4ee647ee0d1c7b035",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621800742"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.72.0",
      "date": "2026-05-29T06:29:10.000Z",
      "commit": "8d3540e6fa9bf775a2c8d9247c475836e768bcd8",
      "fileid": "9894b4c1f230f2802a7a8a4da8397304a58873c568098692992fe785a6dfe723",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621800742"
    }
  ]
}