{
  "_id": "6a17dbe5acfb0bcc41d9c191",
  "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",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-28 06:04:39 UTC",
    "User": "root"
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  "MD5sum": "1df562ebfb4b19f1cc020999266f820f",
  "_user": "bioc",
  "_type": "src",
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  "_published": "2026-05-28T06:08:37.484Z",
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    "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",
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  "_maintainer": {
    "name": "Florence Cavalli",
    "email": "florence@ebi.ac.uk"
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  "_selfowned": true,
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    "differentialexpression",
    "multiplecomparison",
    "clustering",
    "reportwriting"
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  "_userbio": {
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    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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    "source": "https://www.bioconductor.org/packages/stats/bioc/SpeCond"
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  "_searchresults": 14,
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  "_assets": [
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    "extra/contents.json",
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    "manual.pdf"
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  "_realowner": "bioc",
  "_cranurl": false,
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    "fitNoPriorWithExclusion",
    "fitPrior",
    "getDefaultParameter",
    "getFullHtmlSpeCondResult",
    "getGeneHtmlPage",
    "getMatrixFromExpressionSet",
    "getProfile",
    "getSpecificOutliersStep1",
    "getSpecificResult",
    "SpeCond",
    "writeGeneResult",
    "writeSpeCondResult",
    "writeUniqueProfileSpecificResult"
  ],
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      "name": "expressionSpeCondExample",
      "title": "The expression matrix example used in the SpeCond package",
      "object": "expressionSpeCondExample",
      "file": "expressionSpeCondExample.rdata",
      "class": [
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        "array"
      ],
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        "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"
      ]
    }
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      "created": "2013-11-01 20:11:06",
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