{
  "_id": "6a1b08f21d7bb097a0a053e1",
  "Package": "Cascade",
  "Type": "Package",
  "Title": "Selection, Reverse-Engineering and Prediction in Cascade\nNetworks",
  "Version": "2.4",
  "Date": "2026-04-30",
  "biocViews": "",
  "Authors@R": "c(\nperson(given = \"Frederic\", family= \"Bertrand\", role = c(\"cre\", \"aut\"), email = \"frederic.bertrand@lecnam.net\", comment = c(ORCID = \"0000-0002-0837-8281\")),\nperson(given = \"Myriam\", family= \"Maumy-Bertrand\", role = c(\"aut\"), email = \"myriam.maumy@ehesp.fr\", comment = c(ORCID = \"0000-0002-4615-1512\")),\nperson(given = \"Laurent\", family= \"Vallat\", role = c(\"ctb\"), email = \"vallat@unistra.fr\"),\nperson(given = \"Nicolas\", family= \"Jung\", role = c(\"ctb\"), email = \"nicolas.jung@unistra.fr\"))",
  "Author": "Frederic Bertrand [cre, aut]\n(<https://orcid.org/0000-0002-0837-8281>), Myriam\nMaumy-Bertrand [aut] (<https://orcid.org/0000-0002-4615-1512>),\nLaurent Vallat [ctb], Nicolas Jung [ctb]",
  "Maintainer": "Frederic Bertrand <frederic.bertrand@lecnam.net>",
  "Description": "A modeling tool allowing gene selection, reverse\nengineering, and prediction in cascade networks. Jung, N.,\nBertrand, F., Bahram, S., Vallat, L., and Maumy-Bertrand, M.\n(2014) <doi:10.1093/bioinformatics/btt705>.",
  "License": "GPL (>= 2)",
  "Encoding": "UTF-8",
  "Collate": "Cascade-package.R global.R micro_array.R network.R\nmicro_array-network.R micropredict.R datasets.R",
  "Classification/MSC": "62J05, 62J07, 62J99, 92C42",
  "VignetteBuilder": "R.rsp",
  "RoxygenNote": "7.3.3",
  "URL": "https://fbertran.github.io/Cascade/,\nhttps://github.com/fbertran/Cascade",
  "BugReports": "https://github.com/fbertran/Cascade/issues",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "libglpk-dev libmagick++-dev gsfonts texlive\nlibxml2-dev libssl-dev",
  "Repository": "https://fbertran.r-universe.dev",
  "Date/Publication": "2026-04-30 00:52:12 UTC",
  "RemoteUrl": "https://github.com/fbertran/cascade",
  "RemoteRef": "HEAD",
  "RemoteSha": "6e4baa196f18bdb3f6e63c069d265fc97d71f5c7",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 11:01:38 UTC",
    "User": "root"
  },
  "MD5sum": "fe39b87ae2d9ed286f736250d477ad9c",
  "_user": "fbertran",
  "_type": "src",
  "_file": "Cascade_2.4.tar.gz",
  "_fileid": "9a7a1544db4ee09d97c89c2f963c7a8e7a70f416afe7fa7a8f910a3c82f0e914",
  "_filesize": 1622146,
  "_sha256": "9a7a1544db4ee09d97c89c2f963c7a8e7a70f416afe7fa7a8f910a3c82f0e914",
  "_created": "2026-05-30T11:01:38.000Z",
  "_published": "2026-05-30T15:57:38.076Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78644338815,
      "time": 201,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7307770318"
    },
    {
      "job": 78644338811,
      "time": 182,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307768628"
    },
    {
      "job": 78644338816,
      "time": 136,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7309433785"
    },
    {
      "job": 78644338814,
      "time": 126,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7309434759"
    },
    {
      "job": 78643927444,
      "time": 247,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307707121"
    },
    {
      "job": 78644338810,
      "time": 147,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307765578"
    },
    {
      "job": 78644338838,
      "time": 521,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7307799548"
    },
    {
      "job": 78644338829,
      "time": 353,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7307785035"
    },
    {
      "job": 78644338827,
      "time": 125,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307764538"
    }
  ],
  "_buildurl": "https://github.com/r-universe/fbertran/actions/runs/26681271343",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/fbertran/cascade",
  "_commit": {
    "id": "6e4baa196f18bdb3f6e63c069d265fc97d71f5c7",
    "author": "Frederic Bertrand <frederic.bertrand@lecnam.net>",
    "committer": "Frederic Bertrand <frederic.bertrand@lecnam.net>",
    "message": "Fixed CRAN package load warning\nReplaced broad `igraph` imports with selective namespace imports\nReplaced the remaining broad imports with selective imports or removed them when unused\nRemoved the legacy `inst/animation` saveHTML output that vendored vulnerable jQuery assets.\nMoved the E-MTAB-1475 re-analysis PDF out of the package vignettes\n",
    "time": 1777510332
  },
  "_maintainer": {
    "name": "Frederic Bertrand",
    "email": "frederic.bertrand@lecnam.net",
    "login": "fbertran",
    "orcid": "0000-0002-0837-8281",
    "twitter": "@BertrandFrdric2",
    "description": "Full professor in statistical modelling and data science at the CNAM Paris, France",
    "uuid": 6714333
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "abind",
      "role": "Imports"
    },
    {
      "package": "animation",
      "role": "Imports"
    },
    {
      "package": "cluster",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "lars",
      "role": "Imports"
    },
    {
      "package": "lattice",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "nnls",
      "role": "Imports"
    },
    {
      "package": "splines",
      "role": "Imports"
    },
    {
      "package": "stats4",
      "role": "Imports"
    },
    {
      "package": "tnet",
      "role": "Imports"
    },
    {
      "package": "VGAM",
      "role": "Imports"
    },
    {
      "package": "R.rsp",
      "role": "Suggests"
    },
    {
      "package": "CascadeData",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "fbertran",
  "_selfowned": true,
  "_usedby": 4,
  "_updates": [
    {
      "week": "2025-34",
      "n": 2
    },
    {
      "week": "2025-38",
      "n": 2
    },
    {
      "week": "2025-39",
      "n": 1
    },
    {
      "week": "2026-17",
      "n": 7
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_stars": 1,
  "_contributors": [
    {
      "user": "fbertran",
      "count": 54,
      "uuid": 6714333
    }
  ],
  "_userbio": {
    "uuid": 6714333,
    "type": "user",
    "name": "Frederic Bertrand",
    "description": "Full professor in statistical modelling and data science at the CNAM Paris, France"
  },
  "_downloads": {
    "count": 687,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/Cascade"
  },
  "_mentions": 64,
  "_devurl": "https://github.com/fbertran/cascade",
  "_pkgdown": "https://fbertran.github.io/Cascade/",
  "_searchresults": 46,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/Cascade.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/fbertran/cascade",
  "_realowner": "fbertran",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.7",
      "date": "2019-02-18"
    },
    {
      "version": "1.8",
      "date": "2019-08-24"
    },
    {
      "version": "2.0",
      "date": "2021-03-19"
    },
    {
      "version": "2.1",
      "date": "2022-11-28"
    },
    {
      "version": "2.2",
      "date": "2025-08-21"
    },
    {
      "version": "2.3",
      "date": "2025-09-19"
    },
    {
      "version": "2.4",
      "date": "2026-04-30"
    }
  ],
  "_exports": [
    "analyze_network",
    "as.micro_array",
    "compare",
    "cutoff",
    "evolution",
    "gene_expr_simulation",
    "geneNeighborhood",
    "genePeakSelection",
    "geneSelection",
    "head",
    "inference",
    "network_random",
    "plot",
    "position",
    "predict",
    "print",
    "summary",
    "unionMicro"
  ],
  "_datasets": [
    {
      "name": "M",
      "title": "Simulated M data for examples.",
      "object": "M",
      "file": "M.RData",
      "class": [
        "micro_array"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "Net",
      "title": "Simulated network data for examples.",
      "object": "Net",
      "file": "Net.RData",
      "class": [
        "network"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "Net_inf",
      "title": "Reverse-engineered network of the simulated data.",
      "object": "Net_inf",
      "file": "Net_inf.RData",
      "class": [
        "network"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "network",
      "title": "A network object data.",
      "object": "network",
      "file": "network.RData",
      "class": [
        "network"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "Selection",
      "title": "Selection of genes.",
      "object": "Selection",
      "file": "Selection.RData",
      "class": [
        "micro_array"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "analyze_network-network-method",
      "title": "Analysing the network",
      "topics": [
        "analyze_network",
        "analyze_network,network-method",
        "analyze_network-methods"
      ]
    },
    {
      "page": "as.micro_array",
      "title": "Coerce a matrix into a micro_array object.",
      "topics": [
        "as.micro_array"
      ]
    },
    {
      "page": "compare-methods",
      "title": "Some basic criteria of comparison between actual and inferred network.",
      "topics": [
        "compare",
        "compare,network,network,numeric-method",
        "compare-methods"
      ]
    },
    {
      "page": "cutoff-network-method",
      "title": "Choose the best cutoff",
      "topics": [
        "cutoff",
        "cutoff,network-method",
        "cutoff-methods"
      ]
    },
    {
      "page": "dim",
      "title": "Dimension of the data",
      "topics": [
        "dim",
        "dim,micro_array-method",
        "dim-methods"
      ]
    },
    {
      "page": "evolution-network-method",
      "title": "See the evolution of the network with change of cutoff",
      "topics": [
        "evolution",
        "evolution,network-method",
        "evolution-methods"
      ]
    },
    {
      "page": "gene_expr_simulation-network-method",
      "title": "Simulates microarray data based on a given network.",
      "topics": [
        "gene_expr_simulation",
        "gene_expr_simulation,network-method",
        "gene_expr_simulation-methods"
      ]
    },
    {
      "page": "geneNeighborhood-network-method",
      "title": "Find the neighborhood of a set of nodes.",
      "topics": [
        "geneNeighborhood",
        "geneNeighborhood,network-method",
        "geneNeighborhood-methods"
      ]
    },
    {
      "page": "geneSelection",
      "title": "Methods for selecting genes",
      "topics": [
        "genePeakSelection",
        "genePeakSelection,micro_array,numeric-method",
        "genePeakSelection-methods",
        "geneSelection",
        "geneSelection,list,list,numeric-method",
        "geneSelection,micro_array,micro_array,numeric-method",
        "geneSelection-methods"
      ]
    },
    {
      "page": "head-micro_array-method",
      "title": "Overview of a micro_array object",
      "topics": [
        "head,ANY-method",
        "head,micro_array-method",
        "head-methods",
        "methods"
      ]
    },
    {
      "page": "inference-micro_array-method",
      "title": "Reverse-engineer the network",
      "topics": [
        "inference",
        "inference,micro_array-method",
        "inference-methods"
      ]
    },
    {
      "page": "M",
      "title": "Simulated M data for examples.",
      "topics": [
        "M"
      ]
    },
    {
      "page": "micro_array-class",
      "title": "Class '\"micro_array\"'",
      "topics": [
        "micro_array-class"
      ]
    },
    {
      "page": "micropredict-class",
      "title": "Class '\"micropredict\"'",
      "topics": [
        "micropredict-class"
      ]
    },
    {
      "page": "Net",
      "title": "Simulated network data for examples.",
      "topics": [
        "Net"
      ]
    },
    {
      "page": "Net_inf",
      "title": "Reverse-engineered network of the simulated data.",
      "topics": [
        "Net_inf"
      ]
    },
    {
      "page": "network",
      "title": "A network object data.",
      "topics": [
        "network"
      ]
    },
    {
      "page": "network_random",
      "title": "Generates a network.",
      "topics": [
        "network_random"
      ]
    },
    {
      "page": "network-class",
      "title": "Class '\"network\"'",
      "topics": [
        "network-class"
      ]
    },
    {
      "page": "plot-methods",
      "title": "Plot",
      "topics": [
        "plot,ANY,ANY-method",
        "plot,micropredict,ANY-method",
        "plot,micro_array,ANY-method",
        "plot,network,ANY-method",
        "plot-methods"
      ]
    },
    {
      "page": "position-methods",
      "title": "Returns the position of edges in the network",
      "topics": [
        "position",
        "position,network-method",
        "position-methods"
      ]
    },
    {
      "page": "predict-micro_array-method",
      "title": "Prediction of the gene expressions after a knock-out experience 'predict'",
      "topics": [
        "predict",
        "predict,ANY-method",
        "predict,micro_array-method",
        "predict-methods"
      ]
    },
    {
      "page": "print-methods",
      "title": "Methods for Function 'print'",
      "topics": [
        "print,ANY-method",
        "print,micro_array-method",
        "print,network-method",
        "print-methods"
      ]
    },
    {
      "page": "Selection",
      "title": "Selection of genes.",
      "topics": [
        "Selection"
      ]
    },
    {
      "page": "summary-methods",
      "title": "Methods for Function 'summary'",
      "topics": [
        "summary,ANY-method",
        "summary,micro_array-method",
        "summary-methods"
      ]
    },
    {
      "page": "unionMicro-methods",
      "title": "Makes the union between two micro_array objects.",
      "topics": [
        "unionMicro",
        "unionMicro,list,ANY-method",
        "unionMicro,micro_array,micro_array-method",
        "unionMicro-methods"
      ]
    }
  ],
  "_pkglogo": "https://github.com/fbertran/cascade/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/fbertran/cascade/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "animation",
    "cli",
    "cluster",
    "cpp11",
    "curl",
    "glue",
    "igraph",
    "lars",
    "lattice",
    "lifecycle",
    "limma",
    "magick",
    "magrittr",
    "Matrix",
    "nnls",
    "pkgconfig",
    "Rcpp",
    "rlang",
    "statmod",
    "survival",
    "tnet",
    "vctrs",
    "VGAM"
  ],
  "_vignettes": [
    {
      "source": "Cascade.pdf.asis",
      "filename": "Cascade.pdf",
      "title": "Cascade: Introduction to Cascade",
      "engine": "R.rsp::asis",
      "headings": [],
      "created": "2019-01-27 10:42:59",
      "modified": "2019-01-27 10:42:59",
      "commits": 1
    },
    {
      "source": "Cascade-manual.pdf.asis",
      "filename": "Cascade-manual.pdf",
      "title": "Cascade: Manual",
      "engine": "R.rsp::asis",
      "headings": [],
      "created": "2019-01-27 10:42:59",
      "modified": "2019-01-27 10:42:59",
      "commits": 1
    }
  ],
  "_score": 7.440909082065218,
  "_indexed": true,
  "_nocasepkg": "cascade",
  "_universes": [
    "fbertran"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.4",
      "date": "2026-05-30T11:13:00.000Z",
      "distro": "noble",
      "commit": "6e4baa196f18bdb3f6e63c069d265fc97d71f5c7",
      "fileid": "cf21b84ea64157af2519dec58a5e23d63c474884779832af9777e979ccdddd06",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fbertran/actions/runs/26681271343"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.4",
      "date": "2026-05-30T11:12:59.000Z",
      "distro": "noble",
      "commit": "6e4baa196f18bdb3f6e63c069d265fc97d71f5c7",
      "fileid": "67cebcb5ceef557ca7190bf224d7b2ab1f5b3a456d18c0068f5f1667e6a28ddb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fbertran/actions/runs/26681271343"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.4",
      "date": "2026-05-30T15:56:33.000Z",
      "commit": "6e4baa196f18bdb3f6e63c069d265fc97d71f5c7",
      "fileid": "6bb881a690e60ece155a3a097f14d59ba04c0eddf49e7948443638eaa36761c6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fbertran/actions/runs/26681271343"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.4",
      "date": "2026-05-30T15:56:44.000Z",
      "commit": "6e4baa196f18bdb3f6e63c069d265fc97d71f5c7",
      "fileid": "568603f643b9fe2f593113ec1813170be9b59da3284847e4de72ef31ba9d4509",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fbertran/actions/runs/26681271343"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.4",
      "date": "2026-05-30T11:12:55.000Z",
      "commit": "6e4baa196f18bdb3f6e63c069d265fc97d71f5c7",
      "fileid": "56bc92838a4e0f08bfebf93a607cbac52e5660e7ff3991e2597608d9cf176bad",
      "status": "success",
      "buildurl": "https://github.com/r-universe/fbertran/actions/runs/26681271343"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.4",
      "date": "2026-05-30T11:18:24.000Z",
      "commit": "6e4baa196f18bdb3f6e63c069d265fc97d71f5c7",
      "fileid": "a8aa5179927244b003258800f7484647240405fa18204a0f31dd355d604fec0e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fbertran/actions/runs/26681271343"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.4",
      "date": "2026-05-30T11:15:44.000Z",
      "commit": "6e4baa196f18bdb3f6e63c069d265fc97d71f5c7",
      "fileid": "ced55cbdaf9ec08be3b949d4f3fb0aed5ae9416d8424b97bf7ceadd4e77fef8f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fbertran/actions/runs/26681271343"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.4",
      "date": "2026-05-30T11:11:43.000Z",
      "commit": "6e4baa196f18bdb3f6e63c069d265fc97d71f5c7",
      "fileid": "b2a07de90d1ee5be5304d08b3cfcc0806876902aa684bc0aa511c95bffd0c153",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fbertran/actions/runs/26681271343"
    }
  ]
}