{
  "_id": "6a17ecbaacfb0bcc41da46c7",
  "Package": "fcros",
  "Version": "1.6-6",
  "Date": "2026-01-26",
  "Title": "A Method to Search for Differentially Expressed Genes and to\nDetect Recurrent Chromosomal Copy Number Aberrations",
  "Authors@R": "person(given = \"Doulaye\",\nfamily = \"Dembele\",\nrole = c(\"aut\", \"cre\"),\nemail = \"doulaye@igbmc.fr\")",
  "Author": "Doulaye Dembele [aut, cre]",
  "Maintainer": "Doulaye Dembele <doulaye@igbmc.fr>",
  "Description": "A fold change rank based method is presented to search for\ngenes with changing expression and to detect recurrent\nchromosomal copy number aberrations. This method may be useful\nfor high-throughput biological data (micro-array, sequencing,\n...). Probabilities are associated with genes or probes in the\ndata set and there is no problem of multiple tests when using\nthis method. For array-based comparative genomic hybridization\ndata, segmentation results are obtained by merging the\nsignificant probes detected.",
  "License": "GPL (>= 2)",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-28 07:09:50 UTC",
    "User": "root"
  },
  "Repository": "https://doulaye.r-universe.dev",
  "Date/Publication": "2026-01-27 09:10:02 UTC",
  "RemoteUrl": "https://github.com/cran/fcros",
  "RemoteRef": "HEAD",
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  "_published": "2026-05-28T07:20:26.705Z",
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  "_status": "success",
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    "author": "Doulaye Dembele <doulaye@igbmc.fr>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.6-6\n",
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    "email": "doulaye@igbmc.fr",
    "login": "doulaye",
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  "_selfowned": true,
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      "count": 17,
      "uuid": 43007313
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  "_userbio": {
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    "type": "user",
    "name": "Doulaye"
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  "_downloads": {
    "count": 240,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/fcros"
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  "_mentions": 6,
  "_searchresults": 39,
  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/fcros.html",
    "manual.pdf"
  ],
  "_realowner": "doulaye",
  "_cranurl": false,
  "_releases": [
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      "version": "0.9",
      "date": "2013-06-21"
    },
    {
      "version": "1.0",
      "date": "2013-07-29"
    },
    {
      "version": "1.1",
      "date": "2014-01-20"
    },
    {
      "version": "1.2",
      "date": "2014-09-09"
    },
    {
      "version": "1.3",
      "date": "2014-11-28"
    },
    {
      "version": "1.4",
      "date": "2015-07-29"
    },
    {
      "version": "1.4.1",
      "date": "2015-11-08"
    },
    {
      "version": "1.5",
      "date": "2016-07-01"
    },
    {
      "version": "1.5.1",
      "date": "2016-10-10"
    },
    {
      "version": "1.5.2",
      "date": "2016-11-17"
    },
    {
      "version": "1.5.3",
      "date": "2017-04-03"
    },
    {
      "version": "1.5.4",
      "date": "2017-04-14"
    },
    {
      "version": "1.5.5",
      "date": "2017-11-16"
    },
    {
      "version": "1.5.6",
      "date": "2018-03-28"
    },
    {
      "version": "1.6",
      "date": "2019-02-01"
    },
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      "date": "2019-05-31"
    },
    {
      "version": "1.6-6",
      "date": "2026-01-27"
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  ],
  "_exports": [
    "calcSRmat",
    "calcSRmatMod",
    "chrMerge",
    "chrPlot",
    "chrPlot2",
    "chrSegment",
    "dataSummary",
    "fc2Calc",
    "fcros",
    "fcros2",
    "fcrosFCmat",
    "fcrosMod",
    "fcrosRead",
    "fcrosTopN",
    "fcrosTtest",
    "fcrosWrite",
    "fvalTopN",
    "fvalVolcanoPlot",
    "histoPlot",
    "moyStdCalc",
    "pfco",
    "pfcoMod",
    "pvalTopN",
    "pvalVolcanoPlot",
    "rankReads",
    "rmatCalc",
    "rmatTrim",
    "scoreThr",
    "tcnReads",
    "tprobaCalc",
    "varBeta",
    "voomReads"
  ],
  "_datasets": [
    {
      "name": "bott",
      "title": "Example of sequencing data to test the rankReads function.",
      "object": "bott",
      "file": "bott.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "gene",
        "SRX033480",
        "SRX033488",
        "SRX033481",
        "SRX033493",
        "SRX033486",
        "SRX033494"
      ],
      "rows": 5000,
      "table": true,
      "tojson": true
    },
    {
      "name": "cghData",
      "title": "Example of aCGH \"data file\" for the fcros package.",
      "object": "cghData",
      "file": "cghData.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Probes",
        "GSM447252",
        "GSM447253",
        "GSM447254",
        "GSM447255",
        "GSM447256",
        "GSM447257",
        "GSM447258",
        "GSM447259",
        "GSM447260",
        "GSM447261"
      ],
      "rows": 33614,
      "table": true,
      "tojson": true
    },
    {
      "name": "cghInfo",
      "title": "Example of aCGH \"info file\" for the fcros package.",
      "object": "cghInfo",
      "file": "cghInfo.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Index",
        "ProbeName",
        "GeneSymbol",
        "Chromosome",
        "Start",
        "End",
        "Cytoband"
      ],
      "rows": 33614,
      "table": true,
      "tojson": true
    },
    {
      "name": "fdata",
      "title": "Example of dataset for the fcros package.",
      "object": "fdata",
      "file": "fdata.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "index",
        "cont01",
        "cont02",
        "cont03",
        "cont04",
        "cont05",
        "cont06",
        "cont07",
        "cont08",
        "cont09",
        "cont10",
        "test01",
        "test02",
        "test03",
        "test04",
        "test05",
        "test06",
        "test07",
        "test08",
        "test09",
        "test10",
        "DE_status"
      ],
      "rows": 10000,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "fcros-package",
      "title": "A Method to Search for Differentially Expressed Genes and to Detect Recurrent Chromosomal Copy Number Aberrations",
      "topics": [
        "fcros-package"
      ]
    },
    {
      "page": "bott",
      "title": "Example of sequencing data to test the rankReads function.",
      "topics": [
        "bott"
      ]
    },
    {
      "page": "calcSRmat",
      "title": "Calculation of the sorted rank matrix from the dataset",
      "topics": [
        "calcSRmat"
      ]
    },
    {
      "page": "calcSRmatMod",
      "title": "Calculation of the sorted rank matrix from the dataset",
      "topics": [
        "calcSRmatMod"
      ]
    },
    {
      "page": "cghData",
      "title": "Example of aCGH \"data file\" for the fcros package.",
      "topics": [
        "cghData"
      ]
    },
    {
      "page": "cghInfo",
      "title": "Example of aCGH \"info file\" for the fcros package.",
      "topics": [
        "cghInfo"
      ]
    },
    {
      "page": "chrMerge",
      "title": "Using a C code for merging chromosome segments",
      "topics": [
        "chrMerge"
      ]
    },
    {
      "page": "chrPlot",
      "title": "Plot a chromosome data",
      "topics": [
        "chrPlot"
      ]
    },
    {
      "page": "chrPlot2",
      "title": "Plot a chromosome segmentation results",
      "topics": [
        "chrPlot2"
      ]
    },
    {
      "page": "chrSegment",
      "title": "Segmentation of a chromosome data",
      "topics": [
        "chrSegment"
      ]
    },
    {
      "page": "dataSummary",
      "title": "Summarization of the detection results for a list of chromosomes",
      "topics": [
        "dataSummary"
      ]
    },
    {
      "page": "fc2Calc",
      "title": "Calculation of fold change using pairwise comparison values",
      "topics": [
        "fc2Calc"
      ]
    },
    {
      "page": "fcros",
      "title": "Search for differentially expressed genes/probes",
      "topics": [
        "fcros"
      ]
    },
    {
      "page": "fcros2",
      "title": "Search for differentially expressed genes/probes",
      "topics": [
        "fcros2"
      ]
    },
    {
      "page": "fcrosC",
      "title": "Search for differentially expressed genes/probes",
      "topics": [
        "fcrosC"
      ]
    },
    {
      "page": "fcrosFCmat",
      "title": "Calculation of a matrix of fold changes using pairwise comparisons",
      "topics": [
        "fcrosFCmat"
      ]
    },
    {
      "page": "fcrosMod",
      "title": "Search for differentially expressed genes or to detect recurrent copy number aberration probes",
      "topics": [
        "fcrosMod"
      ]
    },
    {
      "page": "fcrosRead",
      "title": "Read a tab delimited text file",
      "topics": [
        "fcrosRead"
      ]
    },
    {
      "page": "fcrosTopN",
      "title": "Search for the top N changed genes or probes",
      "topics": [
        "fcrosTopN"
      ]
    },
    {
      "page": "fcrosTtest",
      "title": "Student t-test for detecting differentially expressed genes",
      "topics": [
        "fcrosTtest"
      ]
    },
    {
      "page": "fcrosWrite",
      "title": "Writing the fcros() or pfco() results in a tab delimited text file",
      "topics": [
        "fcrosWrite"
      ]
    },
    {
      "page": "fdata",
      "title": "Example of dataset for the fcros package.",
      "topics": [
        "fdata"
      ]
    },
    {
      "page": "fvalTopN",
      "title": "Search for the top N changed genes or probes using f-values",
      "topics": [
        "fvalTopN"
      ]
    },
    {
      "page": "fvalVolcanoPlot",
      "title": "Performs a volcano plot of the FCROS/PFCO statistics",
      "topics": [
        "fvalVolcanoPlot"
      ]
    },
    {
      "page": "histoPlot",
      "title": "Histogram plot function of the fcros package results",
      "topics": [
        "histoPlot"
      ]
    },
    {
      "page": "moyStdCalc",
      "title": "Calculation of the mean and the standard deviation of the full or reduced matrix of sorted ranks",
      "topics": [
        "moyStdCalc"
      ]
    },
    {
      "page": "pfco",
      "title": "Searching for differentially expressed genes/probes using an approach based on the Perron-Frobenius theorem",
      "topics": [
        "pfco"
      ]
    },
    {
      "page": "pfcoMod",
      "title": "Searching for differentially expressed genes or detecting recurrent copy number aberration probes using an approach based on the Perron-Frobenius theorem",
      "topics": [
        "pfcoMod"
      ]
    },
    {
      "page": "pvalTopN",
      "title": "Search for the top N changed genes or probes using p-values",
      "topics": [
        "pvalTopN"
      ]
    },
    {
      "page": "pvalVolcanoPlot",
      "title": "Performs a volcano plot of the FCROS/PFCO statistics",
      "topics": [
        "pvalVolcanoPlot"
      ]
    },
    {
      "page": "rankReads",
      "title": "This function computes a score to assess the significance of sequencing values",
      "topics": [
        "rankReads"
      ]
    },
    {
      "page": "rmatCalc",
      "title": "Calculation of the FC matrix using pairwise comparisons",
      "topics": [
        "rmatCalc"
      ]
    },
    {
      "page": "rmatTrim",
      "title": "Calculation of the reduced matrix containing sorted rank values",
      "topics": [
        "rmatTrim"
      ]
    },
    {
      "page": "scoreThr",
      "title": "Determine numerically a threshold for the ranking score",
      "topics": [
        "scoreThr"
      ]
    },
    {
      "page": "tcnReads",
      "title": "Performs a total count normalization of reads",
      "topics": [
        "tcnReads"
      ]
    },
    {
      "page": "tprobaCalc",
      "title": "Calculation of the Student one sample test probabilities",
      "topics": [
        "tprobaCalc"
      ]
    },
    {
      "page": "varBeta",
      "title": "Compute variance of a beta distribution from data",
      "topics": [
        "varBeta"
      ]
    },
    {
      "page": "voomReads",
      "title": "Transformation of read count values",
      "topics": [
        "voomReads"
      ]
    }
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