{
  "_id": "6a18061dacfb0bcc41dacde9",
  "Package": "RNAseqNet",
  "Type": "Package",
  "Title": "Log-Linear Poisson Graphical Model with Hot-Deck Multiple\nImputation",
  "Version": "0.1.5",
  "Date": "2024-02-20",
  "Authors@R": "c(person(\"Alyssa\", \"Imbert\", role = c(\"aut\"), email=\"alyssa.imbert@gmail.com\"),\nperson(\"Nathalie\", \"Vialaneix\", role = c(\"aut\", \"cre\"), email=\"nathalie.vialaneix@inrae.fr\"))",
  "Maintainer": "Nathalie Vialaneix <nathalie.vialaneix@inrae.fr>",
  "Description": "Infer log-linear Poisson Graphical Model with an auxiliary\ndata set. Hot-deck multiple imputation method is used to\nimprove the reliability of the inference with an auxiliary\ndataset. Standard log-linear Poisson graphical model can also\nbe used for the inference and the Stability Approach for\nRegularization Selection (StARS) is implemented to drive the\nselection of the regularization parameter. The method is fully\ndescribed in <doi:10.1093/bioinformatics/btx819>.",
  "License": "GPL (>= 3)",
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.1",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-28 09:04:56 UTC",
    "User": "root"
  },
  "Author": "Alyssa Imbert [aut], Nathalie Vialaneix [aut, cre]",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2024-02-21 02:30:09 UTC",
  "RemoteUrl": "https://github.com/cran/RNAseqNet",
  "RemoteRef": "HEAD",
  "RemoteSha": "8aa6fcb521e59cd9bbec73dd44a8351801f4c0ab",
  "MD5sum": "276a376a6116ba1829dc3b2932e6a252",
  "_user": "cran",
  "_type": "src",
  "_file": "RNAseqNet_0.1.5.tar.gz",
  "_fileid": "86ba12da1d5cfe3514b2251635f9976b53c29a1e7c62fb9b36c01ccedd974c17",
  "_filesize": 1343924,
  "_sha256": "86ba12da1d5cfe3514b2251635f9976b53c29a1e7c62fb9b36c01ccedd974c17",
  "_created": "2026-05-28T09:04:56.000Z",
  "_published": "2026-05-28T09:08:45.583Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78258705057,
      "time": 148,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7261976993"
    },
    {
      "job": 78258705002,
      "time": 167,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7261983039"
    },
    {
      "job": 78258110911,
      "time": 223,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7261929378"
    },
    {
      "job": 78258705024,
      "time": 144,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7261975334"
    }
  ],
  "_buildurl": "https://github.com/r-universe/cran/actions/runs/26565213438",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/RNAseqNet",
  "_commit": {
    "id": "8aa6fcb521e59cd9bbec73dd44a8351801f4c0ab",
    "author": "Nathalie Vialaneix <nathalie.vialaneix@inrae.fr>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 0.1.5\n",
    "time": 1708482609
  },
  "_maintainer": {
    "name": "Nathalie Vialaneix",
    "email": "nathalie.vialaneix@inrae.fr"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.1.0",
      "role": "Depends"
    },
    {
      "package": "ggplot2",
      "role": "Depends"
    },
    {
      "package": "igraph",
      "version": ">= 1.0",
      "role": "Imports"
    },
    {
      "package": "hot.deck",
      "role": "Imports"
    },
    {
      "package": "PoiClaClu",
      "role": "Imports"
    },
    {
      "package": "glmnet",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_userbio": {
    "uuid": 6899542,
    "type": "organization",
    "name": "cran",
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
  "_downloads": {
    "count": 228,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/RNAseqNet"
  },
  "_searchresults": 10,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/RNAseqNet.html",
    "manual.pdf"
  ],
  "_realowner": "cran",
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2017-04-19"
    },
    {
      "version": "0.1.1",
      "date": "2017-05-16"
    },
    {
      "version": "0.1.2",
      "date": "2018-01-19"
    },
    {
      "version": "0.1.3",
      "date": "2020-03-05"
    },
    {
      "version": "0.1.4",
      "date": "2020-06-08"
    },
    {
      "version": "0.1.5",
      "date": "2024-02-20"
    }
  ],
  "_exports": [
    "chooseSigma",
    "GLMnetToGraph",
    "GLMnetwork",
    "imputedGLMnetwork",
    "imputeHD",
    "RNAseqNetUsersGuide",
    "stabilitySelection",
    "varIntra"
  ],
  "_datasets": [
    {
      "name": "lung",
      "title": "RNA-seq expression from lung tissue (GTEx).",
      "object": "lung",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "MT-CO1",
        "SFTPB",
        "SFTPC",
        "MT-ND4",
        "SFTPA2",
        "hsa-mir-6723",
        "SFTPA1",
        "MT-ND5",
        "A2M",
        "MT-CO2",
        "MT-CO3",
        "MT-RNR2",
        "MT-ATP6",
        "MT-ND2",
        "MT-CYB",
        "MT-ND1",
        "FTL",
        "HBB",
        "MTATP6P1",
        "THBS1",
        "MTND2P28",
        "GPX3",
        "ACTB",
        "MT-ND6",
        "FN1",
        "TXNIP",
        "RP5-857K21.7",
        "HSP90AA1",
        "B2M",
        "IGHA1",
        "EPAS1",
        "ZFP36",
        "NEAT1",
        "UBC",
        "SOD2",
        "COL3A1",
        "HLA-E",
        "CD74",
        "TIMP3",
        "SLC34A2",
        "PGC",
        "TIMP1",
        "DCN",
        "COL1A1",
        "IGHG1",
        "HSPA1A",
        "FOS",
        "SERPINE1",
        "RP5-857K21.11",
        "DNAJB1",
        "SAT1",
        "IGHM",
        "HSPA1B",
        "MALAT1",
        "FLNA",
        "GLUL",
        "ACTG1",
        "C10orf10",
        "COL1A2",
        "HBA2",
        "TGM2",
        "CYR61",
        "CTSD",
        "CTSB",
        "TSC22D3",
        "DUSP1",
        "IL1RL1",
        "HLA-B",
        "S100A9",
        "EGR1",
        "AHNAK",
        "FOSB",
        "C3",
        "HSPB1",
        "MYH9",
        "SPARC",
        "RHOB",
        "MTND4P12",
        "AQP1",
        "MFAP4",
        "COL6A3",
        "MT2A",
        "SPARCL1",
        "TMSB4X",
        "HSPA8",
        "NAPSA",
        "PSAP",
        "HLA-C",
        "MACF1",
        "MT-ND4L",
        "HSPA5",
        "SERPINA1",
        "HSP90AB1",
        "ABCA3",
        "S100A8",
        "CD163",
        "HLA-DRA",
        "TNC",
        "MTND1P23",
        "LUM"
      ],
      "rows": 221,
      "table": true,
      "tojson": true
    },
    {
      "name": "thyroid",
      "title": "RNA-seq expression from thyroid tissue (GTEx).",
      "object": "thyroid",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "TG",
        "MT-CO1",
        "MT-ND4",
        "hsa-mir-6723",
        "MT-CO3",
        "MT-CYB",
        "NEAT1",
        "MT-ATP6",
        "MT-CO2",
        "MT-RNR2",
        "MT-ND5",
        "MT-ND2",
        "TPO",
        "MT-ND1",
        "MTATP6P1",
        "GPX3",
        "IGHG1",
        "MTND2P28",
        "RP5-857K21.7",
        "RP5-857K21.11",
        "CTSB",
        "MT-ND6",
        "HBB",
        "MALAT1",
        "CLU",
        "HSP90B1",
        "FTL",
        "TXNIP",
        "IGFBP5",
        "MT-ND4L",
        "MTND4P12",
        "HSP90AA1",
        "GNAS",
        "MT-ND3",
        "EGR1",
        "PRL",
        "HSPA5",
        "IGHA1",
        "UBC",
        "EEF1A1",
        "SFTPB",
        "B2M",
        "GSN",
        "CYR61",
        "DCN",
        "ZFP36",
        "SLC25A29",
        "MT-ATP8",
        "IQGAP1",
        "IYD"
      ],
      "rows": 221,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "chooseSigma",
      "title": "Select the threshold sigma for hd-MI.",
      "topics": [
        "chooseSigma"
      ]
    },
    {
      "page": "GLMnetToGraph",
      "title": "Convert the result of imputedGLMnetwork or a matrix into a network.",
      "topics": [
        "GLMnetToGraph"
      ]
    },
    {
      "page": "GLMnetwork",
      "title": "Infer a network from RNA-seq expression.",
      "topics": [
        "GLMnetwork"
      ]
    },
    {
      "page": "GLMpath",
      "title": "Methods for 'GLMpath' objects.",
      "topics": [
        "GLMpath",
        "GLMpath-class",
        "print.GLMpath",
        "summary.GLMpath"
      ]
    },
    {
      "page": "HDImputed",
      "title": "Methods for 'HDImputed' objects.",
      "topics": [
        "HDImputed",
        "HDImputed-class",
        "print.HDImputed",
        "summary.HDImputed",
        "summary.HDimputed"
      ]
    },
    {
      "page": "HDpath",
      "title": "Methods for 'HDpath' objects.",
      "topics": [
        "HDpath",
        "HDpath-class",
        "plot.HDpath",
        "print.HDpath",
        "summary.HDpath"
      ]
    },
    {
      "page": "imputedGLMnetwork",
      "title": "Multiple hot-deck imputation and network inference from RNA-seq data.",
      "topics": [
        "imputedGLMnetwork"
      ]
    },
    {
      "page": "imputeHD",
      "title": "Impute missing row datasets with multiple hot deck.",
      "topics": [
        "imputeHD"
      ]
    },
    {
      "page": "lung",
      "title": "RNA-seq expression from lung tissue (GTEx).",
      "topics": [
        "lung"
      ]
    },
    {
      "page": "RNAseqNetUsersGuide",
      "title": "View RNAseqNet User's Guide",
      "topics": [
        "RNAseqNetUsersGuide"
      ]
    },
    {
      "page": "stabilitySelection",
      "title": "Selection of the regularization parameter by StARS (Liu et al., 2010).",
      "topics": [
        "stabilitySelection"
      ]
    },
    {
      "page": "stars",
      "title": "Methods for 'stars' objects.",
      "topics": [
        "plot.stars",
        "print.stars",
        "stars",
        "stars-class",
        "summary.stars"
      ]
    },
    {
      "page": "thyroid",
      "title": "RNA-seq expression from thyroid tissue (GTEx).",
      "topics": [
        "thyroid"
      ]
    },
    {
      "page": "varIntra",
      "title": "Average intra-donor pool variance.",
      "topics": [
        "varIntra"
      ]
    }
  ],
  "_rundeps": [
    "backports",
    "bit",
    "bit64",
    "boot",
    "broom",
    "cli",
    "clipr",
    "codetools",
    "cpp11",
    "crayon",
    "data.table",
    "dplyr",
    "farver",
    "forcats",
    "foreach",
    "generics",
    "ggplot2",
    "glmnet",
    "glue",
    "gtable",
    "haven",
    "hms",
    "hot.deck",
    "igraph",
    "isoband",
    "iterators",
    "jomo",
    "labeling",
    "lattice",
    "lifecycle",
    "lme4",
    "magrittr",
    "MASS",
    "Matrix",
    "mice",
    "minqa",
    "mitml",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "ordinal",
    "pan",
    "pillar",
    "pkgconfig",
    "PoiClaClu",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "Rdpack",
    "readr",
    "reformulas",
    "rlang",
    "rpart",
    "S7",
    "scales",
    "shape",
    "stringi",
    "stringr",
    "survival",
    "tibble",
    "tidyr",
    "tidyselect",
    "tzdb",
    "ucminf",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "RNAseqNet.Rmd",
      "filename": "RNAseqNet.html",
      "title": "Log-Linear Poisson Graphical Model with Hot-Deck Multiple Imputation",
      "author": "Nathalie Vialaneix, Alyssa Imbert",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Description",
        "Reference",
        "Session information for the vignette"
      ],
      "created": "2017-05-16 13:40:26",
      "modified": "2020-03-05 13:30:05",
      "commits": 3
    }
  ],
  "_score": 2,
  "_indexed": true,
  "_nocasepkg": "rnaseqnet",
  "_universes": [
    "cran"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.5",
      "date": "2026-05-28T09:07:12.000Z",
      "distro": "noble",
      "commit": "8aa6fcb521e59cd9bbec73dd44a8351801f4c0ab",
      "fileid": "553df8a0b884dd936be826adade8a927aa0de9f7941189852ac9d4b257b7ef32",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26565213438"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.1.5",
      "date": "2026-05-28T09:07:26.000Z",
      "distro": "noble",
      "commit": "8aa6fcb521e59cd9bbec73dd44a8351801f4c0ab",
      "fileid": "e224e9c62213e153888bd4ce7351e0b216e287876d71d7aac035ca36159090a3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26565213438"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.5",
      "date": "2026-05-28T09:07:48.000Z",
      "commit": "8aa6fcb521e59cd9bbec73dd44a8351801f4c0ab",
      "fileid": "19d742cb06a30fb740f22e48e30b93d516a2a56247f011164ac3fcb81facc88e",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26565213438"
    }
  ]
}