{
  "_id": "6a4943a018cdde069385eccf",
  "Package": "SpeCond",
  "Title": "Condition specific detection from expression data",
  "Version": "1.67.0",
  "Author": "Florence Cavalli",
  "Maintainer": "Florence Cavalli <florence@ebi.ac.uk>",
  "Date": "2009-10-13",
  "Import": "mclust, hwriter, RColorBrewer, fields, methods",
  "Collate": "allClass.R show_methods.R fct_SpeCond_2.R\nfct_SpeCond_visualisation.R",
  "Description": "This package performs a gene expression data analysis to\ndetect condition-specific genes. Such genes are significantly\nup- or down-regulated in a small number of conditions. It does\nso by fitting a mixture of normal distributions to the\nexpression values. Conditions can be environmental conditions,\ndifferent tissues, organs or any other sources that you wish to\ncompare in terms of gene expression.",
  "License": "LGPL (>=2)",
  "biocViews": "Microarray, DifferentialExpression, MultipleComparison,\nClustering, ReportWriting",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:34:21 UTC",
  "RemoteUrl": "https://github.com/bioc/SpeCond",
  "RemoteRef": "HEAD",
  "RemoteSha": "4208a6d4e7582823f2a4c493b036d3e6c245ba17",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-04 13:14:10 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "SpeCond_1.67.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/545c6488113bae267243aafcd455982d244acf1b108a18ee0b3eea734de344d4",
  "_filesize": 1927392,
  "_sha256": "545c6488113bae267243aafcd455982d244acf1b108a18ee0b3eea734de344d4",
  "_expires": "2026-10-12T17:32:14.000Z",
  "_created": "2026-07-04T13:14:10.000Z",
  "_published": "2026-07-04T17:32:16.031Z",
  "_bioccheck": {
    "error": 1,
    "warning": 2,
    "note": 15
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28707275545",
  "_status": "success",
  "_upstream": "https://github.com/bioc/SpeCond",
  "_commit": {
    "id": "4208a6d4e7582823f2a4c493b036d3e6c245ba17",
    "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": 1777379661
  },
  "_maintainer": {
    "name": "Florence Cavalli",
    "email": "florence@ebi.ac.uk"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85152499622,
      "time": 138,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8082033355"
    },
    {
      "job": 85152499708,
      "time": 203,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8082040485"
    },
    {
      "job": 85152499667,
      "time": 169,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8082036755"
    },
    {
      "job": 85152499674,
      "time": 90,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8082032053"
    },
    {
      "job": 85152499688,
      "time": 88,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8082032151"
    },
    {
      "job": 85152499436,
      "time": 195,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8082018475"
    },
    {
      "job": 85152499580,
      "time": 142,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8082033662"
    },
    {
      "job": 85152499560,
      "time": 114,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8082031047"
    },
    {
      "job": 85152499589,
      "time": 122,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8082031912"
    },
    {
      "job": 85152499532,
      "time": 166,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8082036671"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.10.0",
      "role": "Depends"
    },
    {
      "package": "mclust",
      "version": ">= 3.3.1",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "version": ">= 1.15.13",
      "role": "Depends"
    },
    {
      "package": "fields",
      "role": "Depends"
    },
    {
      "package": "hwriter",
      "version": ">= 1.1",
      "role": "Depends"
    },
    {
      "package": "RColorBrewer",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.67.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.66.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "microarray",
    "differentialexpression",
    "multiplecomparison",
    "clustering",
    "reportwriting"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_mentions": 3,
  "_searchresults": 14,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/SpeCond.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "createParameterMatrix",
    "fitNoPriorWithExclusion",
    "fitPrior",
    "getDefaultParameter",
    "getFullHtmlSpeCondResult",
    "getGeneHtmlPage",
    "getMatrixFromExpressionSet",
    "getProfile",
    "getSpecificOutliersStep1",
    "getSpecificResult",
    "SpeCond",
    "writeGeneResult",
    "writeSpeCondResult",
    "writeUniqueProfileSpecificResult"
  ],
  "_datasets": [
    {
      "name": "expressionSpeCondExample",
      "title": "The expression matrix example used in the SpeCond package",
      "object": "expressionSpeCondExample",
      "file": "expressionSpeCondExample.rdata",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "Spinal_cord",
        "Fetal_brain",
        "Adrenal_cortex",
        "Pituitary",
        "Whole_brain",
        "Lymph_node",
        "Liver",
        "Prostate",
        "Uterus",
        "Fetal_lung",
        "Appendix",
        "Fetal_thyroid",
        "Heart",
        "Lung",
        "Ovary",
        "Placenta",
        "Pancreas",
        "Skeletal_muscle",
        "Smooth_muscle",
        "Tongue",
        "Thyroid",
        "Tonsil",
        "Whole_blood",
        "Adrenal_gland",
        "Bone_marrow",
        "Fetal_liver",
        "Kidney",
        "Salivary_gland",
        "Skin",
        "Testis",
        "Thymus",
        "Trachea"
      ],
      "rows": 220,
      "table": true,
      "tojson": true
    },
    {
      "name": "expSetSpeCondExample",
      "title": "An ExpressionSet example object used in the SpeCond package",
      "object": "expSetSpeCondExample",
      "file": "expSetSpeCondExample.rdata",
      "class": [
        "ExpressionSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "simulatedSpeCondData",
      "title": "An example of simulated expression matrix used in the SpeCond package",
      "object": "simulatedSpeCondData",
      "file": "simulatedSpeCondData.rdata",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "tissue_1",
        "tissue_2",
        "tissue_3",
        "tissue_4",
        "tissue_5",
        "tissue_6",
        "tissue_7",
        "tissue_8",
        "tissue_9",
        "tissue_10",
        "tissue_11",
        "tissue_12",
        "tissue_13",
        "tissue_14",
        "tissue_15",
        "tissue_16",
        "tissue_17",
        "tissue_18",
        "tissue_19",
        "tissue_20",
        "tissue_21",
        "tissue_22",
        "tissue_23",
        "tissue_24",
        "tissue_25",
        "tissue_26",
        "tissue_27",
        "tissue_28",
        "tissue_29",
        "tissue_30"
      ],
      "rows": 600,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "createParameterMatrix",
      "title": "Create or Modify the SpeCond argument parameters",
      "topics": [
        "createParameterMatrix"
      ]
    },
    {
      "page": "expressionSpeCondExample",
      "title": "The expression matrix example used in the SpeCond package",
      "topics": [
        "expressionSpeCondExample"
      ]
    },
    {
      "page": "expSetSpeCondExample",
      "title": "An ExpressionSet example object used in the SpeCond package",
      "topics": [
        "expSetSpeCondExample"
      ]
    },
    {
      "page": "fitNoPriorWithExclusion",
      "title": "Fit the expression values profile with a mixture of normal components ignoring outliers",
      "topics": [
        "fitNoPriorWithExclusion"
      ]
    },
    {
      "page": "fitPrior",
      "title": "Fit the expression value profiles with a mixture of normal components",
      "topics": [
        "fitPrior"
      ]
    },
    {
      "page": "getDefaultParameter",
      "title": "Get the default parameter to use SpeCond function",
      "topics": [
        "getDefaultParameter"
      ]
    },
    {
      "page": "getFullHtmlSpeCondResult",
      "title": "Visualisation function of the SpeCond analysis results",
      "topics": [
        "getFullHtmlSpeCondResult"
      ]
    },
    {
      "page": "getGeneHtmlPage",
      "title": "Visualise for each gene the condition-specific detection result from SpeCond",
      "topics": [
        "getGeneHtmlPage"
      ]
    },
    {
      "page": "getMatrixFromExpressionSet",
      "title": "Obtain the expression matrix from an ExpressionSet object",
      "topics": [
        "getMatrixFromExpressionSet"
      ]
    },
    {
      "page": "getProfile",
      "title": "Create the condition-specific profile of specific matrix result from SpeCond",
      "topics": [
        "getProfile"
      ]
    },
    {
      "page": "getSpecificOutliersStep1",
      "title": "Detect the condition-specific as outliers in for the first step on the SpeCond procedure",
      "topics": [
        "getSpecificOutliersStep1"
      ]
    },
    {
      "page": "getSpecificResult",
      "title": "Detect the condition-specific genes for the second step on the SpeCond procedure",
      "topics": [
        "getSpecificResult"
      ]
    },
    {
      "page": "simulatedSpeCondData",
      "title": "An example of simulated expression matrix used in the SpeCond package",
      "topics": [
        "simulatedSpeCondData"
      ]
    },
    {
      "page": "SpeCond",
      "title": "The condition-specific detection function",
      "topics": [
        "SpeCond"
      ]
    },
    {
      "page": "writeGeneResult",
      "title": "Write a condition-specific analysis result text file",
      "topics": [
        "writeGeneResult"
      ]
    },
    {
      "page": "writeSpeCondResult",
      "title": "Write in text files the main result of the SpeCond function",
      "topics": [
        "writeSpeCondResult"
      ]
    },
    {
      "page": "writeUniqueProfileSpecificResult",
      "title": "Write the specific profiles from the SpeCond analysis",
      "topics": [
        "writeUniqueProfileSpecificResult"
      ]
    }
  ],
  "_rundeps": [
    "Biobase",
    "BiocGenerics",
    "dotCall64",
    "fields",
    "generics",
    "hwriter",
    "maps",
    "mclust",
    "RColorBrewer",
    "Rcpp",
    "spam",
    "viridisLite"
  ],
  "_vignettes": [
    {
      "source": "SpeCond.Rnw",
      "filename": "SpeCond.pdf",
      "title": "SpeCond",
      "engine": "utils::Sweave",
      "headings": [
        "The detection process in a few words",
        "Quick start",
        "Parameters",
        "More details",
        "Output",
        "Changing the parameter values to improve the detection results",
        "Advice",
        "References"
      ],
      "created": "2013-11-01 20:11:06",
      "modified": "2013-11-01 20:11:06",
      "commits": 1
    }
  ],
  "_score": 3.924279286061882,
  "_indexed": true,
  "_nocasepkg": "specond",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.67.0",
      "date": "2026-07-04T13:17:01.000Z",
      "distro": "resolute",
      "commit": "4208a6d4e7582823f2a4c493b036d3e6c245ba17",
      "fileid": "https://r2.ropensci.org/34c219b03e606547e3b47fde3147d1285b1d5c09370ddefb8897cb3f5a20ad4b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28707275545"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.67.0",
      "date": "2026-07-04T13:16:26.000Z",
      "distro": "resolute",
      "commit": "4208a6d4e7582823f2a4c493b036d3e6c245ba17",
      "fileid": "https://r2.ropensci.org/c510170d45c22b73bbdbf08f2e8d1974bcfba2f911b8d089bce5ebcfad48c5d6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28707275545"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.67.0",
      "date": "2026-07-04T13:16:06.000Z",
      "commit": "4208a6d4e7582823f2a4c493b036d3e6c245ba17",
      "fileid": "https://r2.ropensci.org/5fa0982625d8cf6bd9806d792ee3258d81ad895154bdc43b9150ec1410a3fd5a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28707275545"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.67.0",
      "date": "2026-07-04T13:16:06.000Z",
      "commit": "4208a6d4e7582823f2a4c493b036d3e6c245ba17",
      "fileid": "https://r2.ropensci.org/653aaf4c4cc8af8313292bc0a7894ff3148f44b97cee5b9dd46e02937e17e61c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28707275545"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.67.0",
      "date": "2026-07-04T13:16:47.000Z",
      "commit": "4208a6d4e7582823f2a4c493b036d3e6c245ba17",
      "fileid": "https://r2.ropensci.org/6f368bc32c34ec3a90b166e80f7d19233432f20865b109f6729bcedc2e313c20",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28707275545"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.67.0",
      "date": "2026-07-04T13:15:15.000Z",
      "commit": "4208a6d4e7582823f2a4c493b036d3e6c245ba17",
      "fileid": "https://r2.ropensci.org/f6d25dbe619c093428165942b57a7fb0c3c086f2b3645acda109a4f7abaaad75",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28707275545"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.67.0",
      "date": "2026-07-04T13:15:24.000Z",
      "commit": "4208a6d4e7582823f2a4c493b036d3e6c245ba17",
      "fileid": "https://r2.ropensci.org/448a535c0e7f090657bcde61beabf887fdb37655d304e274aa8b5b48066c06fe",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28707275545"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.67.0",
      "date": "2026-07-04T13:15:43.000Z",
      "commit": "4208a6d4e7582823f2a4c493b036d3e6c245ba17",
      "fileid": "https://r2.ropensci.org/f170268db5254bd8ed6e527abcd577443443aabca8b0a50537979816c57f0b61",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28707275545"
    }
  ]
}