{
  "_id": "6a23e0bb530b9bc726be7ada",
  "Package": "dynafluxr",
  "Type": "Package",
  "Title": "Retrieve Reaction Rate Dynamics from Metabolite Concentration\nTime Courses",
  "Version": "1.0.1",
  "Authors@R": "person(given = \"Serguei\",\nfamily = \"Sokol\",\nrole = c(\"aut\", \"cre\"),\nemail = \"sokol@insa-toulouse.fr\")",
  "Description": "Reaction rate dynamics can be retrieved from metabolite\nconcentration time courses. User has to provide corresponding\nstoichiometric matrix but not a regulation model\n(Michaelis-Menten or similar). Instead of solving an ordinary\ndifferential equation (ODE) system describing the evolution of\nconcentrations, we use B-splines to catch the concentration and\nrate dynamics then solve a least square problem on their\ncoefficients with non-negativity (and optionally monotonicity)\nconstraints. Constraints can be also set on initial values of\nconcentration. The package 'dynafluxr' can be used as a library\nbut also as an application with command line interface\ndynafluxr::cli(\"-h\") or graphical user interface\ndynafluxr::gui().",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.2",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-06 08:53:29 UTC",
    "User": "root"
  },
  "Author": "Serguei Sokol [aut, cre]",
  "Maintainer": "Serguei Sokol <sokol@insa-toulouse.fr>",
  "Config/pak/sysreqs": "cmake make libjpeg-dev libuv1-dev libssl-dev\nzlib1g-dev",
  "Repository": "https://sgsokol.r-universe.dev",
  "Date/Publication": "2025-07-10 14:50:09 UTC",
  "RemoteUrl": "https://github.com/cran/dynafluxr",
  "RemoteRef": "HEAD",
  "RemoteSha": "2f55e54a64957ecc82c4213a98788e1f01c935fc",
  "MD5sum": "26b8060d4c95478a1b31714cee972091",
  "_user": "sgsokol",
  "_type": "src",
  "_file": "dynafluxr_1.0.1.tar.gz",
  "_fileid": "1b155f1bd9e9b3d54afd39f20d1fa075ec0f44175a6c7b043a399c3ff6b757f2",
  "_filesize": 686977,
  "_sha256": "1b155f1bd9e9b3d54afd39f20d1fa075ec0f44175a6c7b043a399c3ff6b757f2",
  "_created": "2026-06-06T08:53:29.000Z",
  "_published": "2026-06-06T08:56:27.364Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79865656095,
      "time": 133,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7453028046"
    },
    {
      "job": 79865656045,
      "time": 143,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7453029105"
    },
    {
      "job": 79865656048,
      "time": 91,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7453023211"
    },
    {
      "job": 79865656047,
      "time": 117,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7453026150"
    },
    {
      "job": 79865477939,
      "time": 188,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7453012419"
    },
    {
      "job": 79865656042,
      "time": 114,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7453025742"
    },
    {
      "job": 79865656055,
      "time": 113,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7453025686"
    },
    {
      "job": 79865656057,
      "time": 83,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7453022187"
    },
    {
      "job": 79865656053,
      "time": 149,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7453029658"
    }
  ],
  "_buildurl": "https://github.com/r-universe/sgsokol/actions/runs/27057883081",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/dynafluxr",
  "_commit": {
    "id": "2f55e54a64957ecc82c4213a98788e1f01c935fc",
    "author": "Serguei Sokol <sokol@insa-toulouse.fr>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.0.1\n",
    "time": 1752159009
  },
  "_maintainer": {
    "name": "Serguei Sokol",
    "email": "sokol@insa-toulouse.fr",
    "login": "sgsokol",
    "description": "",
    "uuid": 9048783
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "bspline",
      "version": ">= 2.5.0",
      "role": "Depends"
    },
    {
      "package": "nlsic",
      "version": ">= 1.1.1",
      "role": "Depends"
    },
    {
      "package": "optparse",
      "role": "Imports"
    },
    {
      "package": "qpdf",
      "role": "Imports"
    },
    {
      "package": "arrApply",
      "role": "Imports"
    },
    {
      "package": "slam",
      "role": "Imports"
    },
    {
      "package": "gmresls",
      "version": ">= 0.2",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "role": "Imports"
    },
    {
      "package": "shinyjs",
      "role": "Imports"
    },
    {
      "package": "shinyFiles",
      "role": "Imports"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-28",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "1.0.1",
      "date": "2025-07-10"
    }
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "sgsokol",
      "count": 1,
      "uuid": 9048783
    }
  ],
  "_userbio": {
    "uuid": 9048783,
    "type": "user",
    "name": "Serguei Sokol"
  },
  "_downloads": {
    "count": 152,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/dynafluxr"
  },
  "_searchresults": 2,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/dynafluxr.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "sgsokol",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0.1",
      "date": "2025-07-10"
    }
  ],
  "_exports": [
    "cli",
    "fdyn",
    "gui",
    "txt2sto"
  ],
  "_help": [
    {
      "page": "cli",
      "title": "Function to be called from shell command line",
      "topics": [
        "cli"
      ]
    },
    {
      "page": "fdyn",
      "title": "Retrieve flux dynamics from metabolic kinetics",
      "topics": [
        "fdyn"
      ]
    },
    {
      "page": "gui",
      "title": "Launch graphical user interface in web browser",
      "topics": [
        "gui"
      ]
    },
    {
      "page": "txt2sto",
      "title": "Translate plain text file with reactions to stoichiometric matrix",
      "topics": [
        "txt2sto"
      ]
    }
  ],
  "_readme": "https://github.com/cran/dynafluxr/raw/HEAD/README.md",
  "_rundeps": [
    "arrApply",
    "askpass",
    "base64enc",
    "bslib",
    "bspline",
    "cachem",
    "cli",
    "commonmark",
    "curl",
    "digest",
    "dotty",
    "fastmap",
    "fontawesome",
    "fs",
    "glue",
    "gmresls",
    "htmltools",
    "httpuv",
    "jquerylib",
    "jsonlite",
    "later",
    "lifecycle",
    "magrittr",
    "memoise",
    "mime",
    "nlsic",
    "nnls",
    "optparse",
    "otel",
    "pillar",
    "pkgconfig",
    "promises",
    "qpdf",
    "R6",
    "rappdirs",
    "Rcpp",
    "RcppArmadillo",
    "rlang",
    "sass",
    "shiny",
    "shinyFiles",
    "shinyjs",
    "slam",
    "sourcetools",
    "sys",
    "tibble",
    "utf8",
    "vctrs",
    "withr",
    "xtable"
  ],
  "_vignettes": [
    {
      "source": "glyco.Rmd",
      "filename": "glyco.html",
      "title": "Metabolic Flux Dynamics in Upper Glycolysis with dynafluxr",
      "author": "Serguei Sokol^[TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France] ^[MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse 31077, France]",
      "engine": "knitr::knitr",
      "headings": [
        "Introduction",
        "Data preparations",
        "Stoichiometric model preparation",
        "Data exploring",
        "First estimate of fluxes with dynafluxr",
        "Getting fit better",
        "Exploring results",
        "Conclusion"
      ],
      "created": "2025-07-10 14:50:09",
      "modified": "2025-07-10 14:50:09",
      "commits": 1
    }
  ],
  "_score": 2.6989700043360187,
  "_indexed": true,
  "_nocasepkg": "dynafluxr",
  "_universes": [
    "sgsokol"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.1",
      "date": "2026-06-06T08:55:36.000Z",
      "distro": "noble",
      "commit": "2f55e54a64957ecc82c4213a98788e1f01c935fc",
      "fileid": "c74fbd497518e7053fde15114652ce8b000cee128bf236022b96595ccfa5a3d5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/sgsokol/actions/runs/27057883081"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.1",
      "date": "2026-06-06T08:55:44.000Z",
      "distro": "noble",
      "commit": "2f55e54a64957ecc82c4213a98788e1f01c935fc",
      "fileid": "72a9ced17df366f9765f497963015affc93ef5b786d655768711999b4540b132",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/sgsokol/actions/runs/27057883081"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.1",
      "date": "2026-06-06T08:54:58.000Z",
      "commit": "2f55e54a64957ecc82c4213a98788e1f01c935fc",
      "fileid": "1c57f81a334852e287d614a59ec4a5a7aaff39b48adbe5dd23fcbbf8d9c7915d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/sgsokol/actions/runs/27057883081"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.1",
      "date": "2026-06-06T08:55:19.000Z",
      "commit": "2f55e54a64957ecc82c4213a98788e1f01c935fc",
      "fileid": "d3e4d02d915cf61e6d8cc3b4a46c818bbad4c67906169b2192fbfbfc9e9d7cb5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/sgsokol/actions/runs/27057883081"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.1",
      "date": "2026-06-06T08:55:39.000Z",
      "commit": "2f55e54a64957ecc82c4213a98788e1f01c935fc",
      "fileid": "c1cd8ee1bc0d664c4d545b90ce6de3a1f2a2b12dc21eab930e90c525f0d65d3d",
      "status": "success",
      "buildurl": "https://github.com/r-universe/sgsokol/actions/runs/27057883081"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.1",
      "date": "2026-06-06T08:55:06.000Z",
      "commit": "2f55e54a64957ecc82c4213a98788e1f01c935fc",
      "fileid": "229fe41cd4d148dc2def1d0aa46b3cd61199efa9738c6b37731e36c3ae064a11",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/sgsokol/actions/runs/27057883081"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.1",
      "date": "2026-06-06T08:54:39.000Z",
      "commit": "2f55e54a64957ecc82c4213a98788e1f01c935fc",
      "fileid": "f135ccfaf7383e56c07ab953f00412f67f3ead696d831b4ea59ef6e2b23d40b8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/sgsokol/actions/runs/27057883081"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.1",
      "date": "2026-06-06T08:55:18.000Z",
      "commit": "2f55e54a64957ecc82c4213a98788e1f01c935fc",
      "fileid": "5abb8727e015c64bf6fe0c07f7eb7840e1af82215e242946a050e62a47708fc4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/sgsokol/actions/runs/27057883081"
    }
  ]
}