{
  "_id": "6a4ddf93d253724d3f6dd89a",
  "Package": "splineTimeR",
  "Type": "Package",
  "Title": "Time-course differential gene expression data analysis using\nspline regression models followed by gene association network\nreconstruction",
  "Version": "1.41.0",
  "Date": "2020-07-16",
  "Author": "Agata Michna",
  "Maintainer": "Herbert Braselmann <hbraselmann@online.de>, Martin\nSelmansberger <martin.selmansberger@helmholtz-muenchen.de>",
  "Description": "This package provides functions for differential gene\nexpression analysis of gene expression time-course data.\nNatural cubic spline regression models are used. Identified\ngenes may further be used for pathway enrichment analysis\nand/or the reconstruction of time dependent gene regulatory\nassociation networks.",
  "License": "GPL-3",
  "biocViews": "GeneExpression, DifferentialExpression, TimeCourse,\nRegression, GeneSetEnrichment, NetworkEnrichment,\nNetworkInference, GraphAndNetwork",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "no",
  "Config/pak/sysreqs": "libglpk-dev libpng-dev libxml2-dev libssl-dev\nzlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:42:22 UTC",
  "RemoteUrl": "https://github.com/bioc/splineTimeR",
  "RemoteRef": "HEAD",
  "RemoteSha": "69a96090b8963ba8aad4c6722f3a6615365e0a3e",
  "Packaged": {
    "Date": "2026-07-08 05:21:22 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "splineTimeR_1.41.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/e5abbc7f43741dae884320e1bc99845b09ab067240458beac046bad791153c93",
  "_filesize": 1278889,
  "_sha256": "e5abbc7f43741dae884320e1bc99845b09ab067240458beac046bad791153c93",
  "_expires": "2026-10-16T05:26:42.000Z",
  "_created": "2026-07-08T05:21:22.000Z",
  "_published": "2026-07-08T05:26:43.694Z",
  "_bioccheck": {
    "error": 2,
    "warning": 1,
    "note": 14
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28919382943",
  "_status": "success",
  "_upstream": "https://github.com/bioc/splineTimeR",
  "_commit": {
    "id": "69a96090b8963ba8aad4c6722f3a6615365e0a3e",
    "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": 1777380142
  },
  "_maintainer": {
    "name": "Herbert Braselmann",
    "email": "martin.selmansberger@helmholtz-muenchen.de",
    "login": "hbrmuc",
    "description": "privat",
    "uuid": 54470535
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 85793596920,
      "time": 177,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8158948592"
    },
    {
      "job": 85793596916,
      "time": 271,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8158973724"
    },
    {
      "job": 85793596919,
      "time": 252,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8158969069"
    },
    {
      "job": 85793596915,
      "time": 199,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8158953871"
    },
    {
      "job": 85793596940,
      "time": 195,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8158953052"
    },
    {
      "job": 85793051993,
      "time": 258,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8158902941"
    },
    {
      "job": 85793596894,
      "time": 147,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8158940531"
    },
    {
      "job": 85793596956,
      "time": 205,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8158956381"
    },
    {
      "job": 85793596959,
      "time": 205,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8158956242"
    },
    {
      "job": 85793596958,
      "time": 229,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8158963083"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.3",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "role": "Depends"
    },
    {
      "package": "igraph",
      "role": "Depends"
    },
    {
      "package": "limma",
      "role": "Depends"
    },
    {
      "package": "GSEABase",
      "role": "Depends"
    },
    {
      "package": "gtools",
      "role": "Depends"
    },
    {
      "package": "splines",
      "role": "Depends"
    },
    {
      "package": "GeneNet",
      "version": ">= 1.2.13",
      "role": "Depends"
    },
    {
      "package": "longitudinal",
      "version": ">= 1.1.12",
      "role": "Depends"
    },
    {
      "package": "FIs",
      "role": "Depends"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.41.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.40.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "geneexpression",
    "differentialexpression",
    "timecourse",
    "regression",
    "genesetenrichment",
    "networkenrichment",
    "networkinference",
    "graphandnetwork"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 445,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 426,
    "source": "https://www.bioconductor.org/packages/stats/bioc/splineTimeR"
  },
  "_mentions": 3,
  "_searchresults": 17,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/splineTimeR.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "networkProperties",
    "pathEnrich",
    "splineDiffExprs",
    "splineNetRecon",
    "splinePlot"
  ],
  "_datasets": [
    {
      "name": "TCsimData",
      "title": "Simulated time-course gene expression data set",
      "object": "TCsimData",
      "file": "TCsimData.rda",
      "class": [
        "ExpressionSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "networkProperties",
      "title": "Scale-free properties of a network",
      "topics": [
        "networkProperties"
      ]
    },
    {
      "page": "pathEnrich",
      "title": "Pathway enrichment analysis",
      "topics": [
        "pathEnrich"
      ]
    },
    {
      "page": "splineDiffExprs",
      "title": "Differential expression analysis based on natural cubic spline regression models for time-course data",
      "topics": [
        "splineDiffExprs"
      ]
    },
    {
      "page": "splineNetRecon",
      "title": "Network reconstruction based on partial correlation method with shrinkage approach",
      "topics": [
        "splineNetRecon"
      ]
    },
    {
      "page": "splinePlot",
      "title": "Plot spline regression curves of time-course data",
      "topics": [
        "splinePlot"
      ]
    },
    {
      "page": "TCsimData",
      "title": "Simulated time-course gene expression data set",
      "topics": [
        "TCsimData"
      ]
    }
  ],
  "_rundeps": [
    "annotate",
    "AnnotationDbi",
    "askpass",
    "Biobase",
    "BiocGenerics",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "corpcor",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "fastmap",
    "fdrtool",
    "FIs",
    "GeneNet",
    "generics",
    "glue",
    "graph",
    "GSEABase",
    "gtools",
    "httr",
    "igraph",
    "IRanges",
    "jsonlite",
    "KEGGREST",
    "lattice",
    "lifecycle",
    "limma",
    "longitudinal",
    "magrittr",
    "Matrix",
    "memoise",
    "mime",
    "openssl",
    "pkgconfig",
    "png",
    "R6",
    "rlang",
    "RSQLite",
    "S4Vectors",
    "Seqinfo",
    "statmod",
    "sys",
    "vctrs",
    "XML",
    "xtable",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "splineTimeR.Rnw",
      "filename": "splineTimeR.pdf",
      "title": "splineTimeR",
      "engine": "utils::Sweave",
      "headings": [
        "Overview",
        "Data preparation",
        "Time-course data differential expression analysis",
        "Visualization of time-course data with natural cubic spline regression model",
        "Pathway enrichment analysis",
        "Gene association network reconstruction of time-course data",
        "Scale-free properties of a network"
      ],
      "created": "2016-03-25 10:26:52",
      "modified": "2016-10-05 12:59:00",
      "commits": 6
    }
  ],
  "_score": 4.008600171761918,
  "_indexed": true,
  "_nocasepkg": "splinetimer",
  "_universes": [
    "bioc",
    "hbrmuc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.41.0",
      "date": "2026-07-08T05:24:37.000Z",
      "distro": "resolute",
      "commit": "69a96090b8963ba8aad4c6722f3a6615365e0a3e",
      "fileid": "https://r2.ropensci.org/46a7b5bec163f4750e4cacba6660fe99cf0784bb4eb88719feee133101565559",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28919382943"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.41.0",
      "date": "2026-07-08T05:24:25.000Z",
      "distro": "resolute",
      "commit": "69a96090b8963ba8aad4c6722f3a6615365e0a3e",
      "fileid": "https://r2.ropensci.org/3623c79929bb56f3dbf876ba7361d01583a008536daa76231a77d9217e331f84",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28919382943"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-07-08T05:23:38.000Z",
      "commit": "69a96090b8963ba8aad4c6722f3a6615365e0a3e",
      "fileid": "https://r2.ropensci.org/fbed8c526932a4cdb23bd94662af0091283102ff48aa20bbb9c42217f0db514d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28919382943"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.41.0",
      "date": "2026-07-08T05:23:28.000Z",
      "commit": "69a96090b8963ba8aad4c6722f3a6615365e0a3e",
      "fileid": "https://r2.ropensci.org/6a9f295b119a15d3771d30d599fa8bd0a448d4e28274e6edc933bc861b2571f2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28919382943"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.41.0",
      "date": "2026-07-08T05:24:14.000Z",
      "commit": "69a96090b8963ba8aad4c6722f3a6615365e0a3e",
      "fileid": "https://r2.ropensci.org/dd2168ff5b1bdb4783cd6c93591455ba7613ee866eb37e24fc0ca5aa78ad88ba",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28919382943"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-07-08T05:22:44.000Z",
      "commit": "69a96090b8963ba8aad4c6722f3a6615365e0a3e",
      "fileid": "https://r2.ropensci.org/1e3279be6ac9a15788bdcdc8ce99c36371f51f9efb288c67dc34dcdd1d42054c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28919382943"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-07-08T05:22:48.000Z",
      "commit": "69a96090b8963ba8aad4c6722f3a6615365e0a3e",
      "fileid": "https://r2.ropensci.org/e3349da50fcf06b6605a38e7b469398e59e61052df670a4fe27e3c653b40f1b0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28919382943"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.41.0",
      "date": "2026-07-08T05:23:13.000Z",
      "commit": "69a96090b8963ba8aad4c6722f3a6615365e0a3e",
      "fileid": "https://r2.ropensci.org/64d58382203f643402689d544a46c47cfdea5aa2f04cee95695b90e2aab9296d",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28919382943"
    }
  ]
}