{
  "_id": "6ac0b40591601a2ad2997947",
  "Package": "RGBM",
  "Type": "Package",
  "Title": "LS-TreeBoost and LAD-TreeBoost for Gene Regulatory Network\nReconstruction",
  "Version": "1.0-11",
  "Date": "2023-04-13",
  "Author": "Raghvendra Mall [aut, cre], Khalid Kunji [aut], Melissa O'Neill\n[ctb]",
  "Authors@R": "c(person(given = \"Raghvendra\",family = \"Mall\",role = c(\"aut\",\"cre\"), email = \"raghvendra5688@gmail.com\"),\nperson(given=\"Khalid\",family=\"Kunji\",role=\"aut\",email = \"kkunji@hbku.edu.qa\"),\nperson(given=\"Melissa\",family=\"O'Neill\",role=\"ctb\"))",
  "Maintainer": "Raghvendra Mall <raghvendra5688@gmail.com>",
  "Description": "Provides an implementation of Regularized LS-TreeBoost &\nLAD-TreeBoost algorithm for Regulatory Network inference from\nany type of expression data (Microarray/RNA-seq etc).",
  "License": "GPL (>= 3)",
  "LazyLoad": "yes",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-03 07:43:48 UTC",
    "User": "root"
  },
  "Repository": "https://raghvendra5688.r-universe.dev",
  "Date/Publication": "2023-04-14 07:50:14 UTC",
  "RemoteUrl": "https://github.com/cran/RGBM",
  "RemoteRef": "HEAD",
  "RemoteSha": "80c5df56a560c2f044dc968bc733d39a306fea8c",
  "_user": "raghvendra5688",
  "_type": "src",
  "_file": "RGBM_1.0-11.tar.gz",
  "_fileid": "https://r2.ropensci.org/fe07aaa3d2667997cb07e72b2b5b5ce8700cd988568467c23c2f6e86693ffecd",
  "_filesize": 174870,
  "_sha256": "fe07aaa3d2667997cb07e72b2b5b5ce8700cd988568467c23c2f6e86693ffecd",
  "_expires": "2027-01-11T07:51:32.000Z",
  "_created": "2026-10-03T07:43:48.000Z",
  "_published": "2026-10-03T07:51:33.683Z",
  "_jobs": [
    {
      "job": 111158312835,
      "time": 77,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11267514151"
    },
    {
      "job": 111158312781,
      "time": 93,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11267948853"
    },
    {
      "job": 111158312786,
      "time": 112,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11268661199"
    },
    {
      "job": 111158312826,
      "time": 91,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11267194425"
    },
    {
      "job": 111158312843,
      "time": 201,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11267124582"
    },
    {
      "job": 111158312859,
      "time": 418,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11268676558"
    },
    {
      "job": 111158312888,
      "time": 131,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11268356598"
    },
    {
      "job": 111158312810,
      "time": 187,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11268381725"
    },
    {
      "job": 111157783051,
      "time": 199,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11268242010"
    },
    {
      "job": 111158312737,
      "time": 114,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11268301926"
    },
    {
      "job": 111158312839,
      "time": 311,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11268601620"
    },
    {
      "job": 111158312840,
      "time": 116,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11268256954"
    },
    {
      "job": 111158312816,
      "time": 72,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11268576320"
    },
    {
      "job": 111158312905,
      "time": 307,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11268920812"
    },
    {
      "job": 111158312827,
      "time": 75,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11267859063"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/raghvendra5688/actions/runs/37107125601",
  "_status": "success",
  "_upstream": "https://github.com/cran/RGBM",
  "_commit": {
    "id": "80c5df56a560c2f044dc968bc733d39a306fea8c",
    "author": "Raghvendra Mall <raghvendra5688@gmail.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.0-11\n",
    "time": 1681458614
  },
  "_maintainer": {
    "name": "Raghvendra Mall",
    "email": "raghvendra5688@gmail.com",
    "login": "raghvendra5688",
    "twitter": "@MallRaghvendra",
    "description": "Applied ML, Computational Biology, Complex Systems",
    "uuid": 3835184
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "foreach",
      "role": "Depends"
    },
    {
      "package": "plyr",
      "role": "Depends"
    },
    {
      "package": "doParallel",
      "role": "Depends"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "raghvendra5688",
      "count": 3,
      "uuid": 3835184
    }
  ],
  "_userbio": {
    "uuid": 3835184,
    "type": "user",
    "name": "Raghevndra Mall",
    "followers": 7,
    "description": "Applied ML, Computational Biology, Complex Systems"
  },
  "_downloads": {
    "count": 434,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/RGBM"
  },
  "_mentions": 1,
  "_searchresults": 4,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/RGBM.html"
  ],
  "_realowner": "raghvendra5688",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0-4",
      "date": "2017-02-21"
    },
    {
      "version": "1.0-5",
      "date": "2017-04-01"
    },
    {
      "version": "1.0-6",
      "date": "2017-04-01"
    },
    {
      "version": "1.0-7",
      "date": "2017-05-08"
    },
    {
      "version": "1.0-8",
      "date": "2018-01-09"
    },
    {
      "version": "1.0-9",
      "date": "2022-08-11"
    },
    {
      "version": "1.0-10",
      "date": "2022-09-26"
    },
    {
      "version": "1.0-11",
      "date": "2023-04-14"
    }
  ],
  "_exports": [
    "add_names",
    "apply_row_deviation",
    "consider_previous_information",
    "first_GBM_step",
    "GBM",
    "GBM.test",
    "GBM.train",
    "get_colids",
    "get_filepaths",
    "get_ko_experiments",
    "get_tf_indices",
    "normalize_matrix_colwise",
    "null_model_refinement_step",
    "regularized_GBM_step",
    "regulate_regulon_size",
    "RGBM",
    "RGBM.test",
    "RGBM.train",
    "second_GBM_step",
    "select_ideal_k",
    "test_regression_stump_R",
    "train_regression_stump_R",
    "transform_importance_to_weights",
    "v2l",
    "z_score_effect"
  ],
  "_help": [
    {
      "page": "add_names",
      "title": "Add row and column names to the adjacency matrix A",
      "topics": [
        "add_names"
      ]
    },
    {
      "page": "apply_row_deviation",
      "title": "Apply row-wise deviation on the inferred GRN",
      "topics": [
        "apply_row_deviation"
      ]
    },
    {
      "page": "consider_previous_information",
      "title": "Remember the intermediate inferred GRN while generating the final inferred GRN",
      "topics": [
        "consider_previous_information"
      ]
    },
    {
      "page": "first_GBM_step",
      "title": "Perform either LS-Boost or LAD-Boost ('GBM') on expression matrix E followed by the 'null_model_refinement_step'",
      "topics": [
        "first_GBM_step"
      ]
    },
    {
      "page": "GBM",
      "title": "Calculate Gene Regulatory Network from Expression data using either LS-TreeBoost or LAD-TreeBoost",
      "topics": [
        "GBM"
      ]
    },
    {
      "page": "GBM.test",
      "title": "Test GBM predictor",
      "topics": [
        "GBM.test"
      ]
    },
    {
      "page": "GBM.train",
      "title": "Train GBM predictor",
      "topics": [
        "GBM.train"
      ]
    },
    {
      "page": "get_colids",
      "title": "Get the indices of recitifed list of Tfs for individual target gene",
      "topics": [
        "get_colids"
      ]
    },
    {
      "page": "get_filepaths",
      "title": "Generate filepaths to maintain adjacency matrices and images",
      "topics": [
        "get_filepaths"
      ]
    },
    {
      "page": "get_ko_experiments",
      "title": "Get indices of experiments where knockout or knockdown happened",
      "topics": [
        "get_ko_experiments"
      ]
    },
    {
      "page": "get_tf_indices",
      "title": "Get the indices of all the TFs from the data",
      "topics": [
        "get_tf_indices"
      ]
    },
    {
      "page": "normalize_matrix_colwise",
      "title": "Column normalize the obtained adjacency matrix",
      "topics": [
        "normalize_matrix_colwise"
      ]
    },
    {
      "page": "null_model_refinement_step",
      "title": "Perform the null model refinement step",
      "topics": [
        "null_model_refinement_step"
      ]
    },
    {
      "page": "regularized_GBM_step",
      "title": "Perform the regularized GBM modelling once the initial GRN is inferred",
      "topics": [
        "regularized_GBM_step"
      ]
    },
    {
      "page": "regulate_regulon_size",
      "title": "Regulate the size of the regulon for each TF",
      "topics": [
        "regulate_regulon_size"
      ]
    },
    {
      "page": "RGBM",
      "title": "Regularized Gradient Boosting Machine for inferring GRN",
      "topics": [
        "RGBM"
      ]
    },
    {
      "page": "RGBM.test",
      "title": "Test rgbm predictor",
      "topics": [
        "RGBM.test"
      ]
    },
    {
      "page": "RGBM.train",
      "title": "Train RGBM predictor",
      "topics": [
        "RGBM.train"
      ]
    },
    {
      "page": "second_GBM_step",
      "title": "Re-iterate through the core GBM model building with optimal set of Tfs for each target gene",
      "topics": [
        "second_GBM_step"
      ]
    },
    {
      "page": "select_ideal_k",
      "title": "Identifies the optimal value of k i.e. top k Tfs for each target gene",
      "topics": [
        "select_ideal_k"
      ]
    },
    {
      "page": "test_regression_stump_R",
      "title": "Test the regression model",
      "topics": [
        "test_regression_stump_R"
      ]
    },
    {
      "page": "train_regression_stump_R",
      "title": "Train the regression stump",
      "topics": [
        "train_regression_stump_R"
      ]
    },
    {
      "page": "transform_importance_to_weights",
      "title": "Log transforms the edge-weights in the inferred GRN",
      "topics": [
        "transform_importance_to_weights"
      ]
    },
    {
      "page": "v2l",
      "title": "Convert adjacency matrix to a list of edges",
      "topics": [
        "v2l"
      ]
    },
    {
      "page": "z_score_effect",
      "title": "Generates a matrix S2 of size Ntfs x Ntargets using the null-mutant zscore algorithm 'Prill, Robert J., et al'",
      "topics": [
        "z_score_effect"
      ]
    }
  ],
  "_rundeps": [
    "codetools",
    "doParallel",
    "foreach",
    "iterators",
    "plyr",
    "Rcpp"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_score": 1,
  "_indexed": true,
  "_nocasepkg": "rgbm",
  "_universes": [
    "raghvendra5688"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0-11",
      "date": "2026-10-03T07:45:17.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "80c5df56a560c2f044dc968bc733d39a306fea8c",
      "fileid": "https://r2.ropensci.org/69e68d6d829e8902424e743af9d05215338052118932eff3d007d4f56d7b2bd3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/raghvendra5688/actions/runs/37107125601"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0-11",
      "date": "2026-10-03T07:45:25.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "80c5df56a560c2f044dc968bc733d39a306fea8c",
      "fileid": "https://r2.ropensci.org/3e37f5830132b2c833c1e5c187d478cdae98a8063277b1f87f7fc708363cb2ea",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/raghvendra5688/actions/runs/37107125601"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.0-11",
      "date": "2026-10-03T07:45:53.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "80c5df56a560c2f044dc968bc733d39a306fea8c",
      "fileid": "https://r2.ropensci.org/062a18a2e01cc6bfe9e1dc6c229c92c88dfad99ee6e214237aa177be41238de2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/raghvendra5688/actions/runs/37107125601"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.0-11",
      "date": "2026-10-03T07:45:30.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "80c5df56a560c2f044dc968bc733d39a306fea8c",
      "fileid": "https://r2.ropensci.org/cb74d394a1eed6b26f6a936f990d7c6fc71356cfdc20b937844b580c4014293e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/raghvendra5688/actions/runs/37107125601"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0-11",
      "date": "2026-10-03T07:46:35.000Z",
      "arch": "aarch64",
      "commit": "80c5df56a560c2f044dc968bc733d39a306fea8c",
      "fileid": "https://r2.ropensci.org/0a67911f4cf1f757342946631df8d87758a4cbf3eaa742ad2a9da2511947e857",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/raghvendra5688/actions/runs/37107125601"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0-11",
      "date": "2026-10-03T07:49:45.000Z",
      "arch": "x86_64",
      "commit": "80c5df56a560c2f044dc968bc733d39a306fea8c",
      "fileid": "https://r2.ropensci.org/75dfdb0d3eeccebba3ba2668eb9b86f912e0909940963e0fb8df442ee329e443",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/raghvendra5688/actions/runs/37107125601"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.0-11",
      "date": "2026-10-03T07:45:46.000Z",
      "arch": "aarch64",
      "commit": "80c5df56a560c2f044dc968bc733d39a306fea8c",
      "fileid": "https://r2.ropensci.org/bebb860660cf0670c296b7c6c7442008f1e9f02648b89d1abc61bdb36e284af1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/raghvendra5688/actions/runs/37107125601"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.0-11",
      "date": "2026-10-03T07:46:24.000Z",
      "arch": "x86_64",
      "commit": "80c5df56a560c2f044dc968bc733d39a306fea8c",
      "fileid": "https://r2.ropensci.org/8eb65d5a193a5fb62583d89627b86ac4aed391a807055073fd5599bb3de15401",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/raghvendra5688/actions/runs/37107125601"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0-11",
      "date": "2026-10-03T07:45:57.000Z",
      "arch": "emscripten",
      "commit": "80c5df56a560c2f044dc968bc733d39a306fea8c",
      "fileid": "https://r2.ropensci.org/3731ecbd1e08c56cd5b2afcce85fbf6021faad990489d865a42fa943495e422b",
      "status": "success",
      "buildurl": "https://github.com/r-universe/raghvendra5688/actions/runs/37107125601"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0-11",
      "date": "2026-10-03T07:48:17.000Z",
      "arch": "aarch64",
      "commit": "80c5df56a560c2f044dc968bc733d39a306fea8c",
      "fileid": "https://r2.ropensci.org/ab8e7546657929ccb2d63b965bd7f2dc1b368c5b2394f7fccba826e0ca0d1cce",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/raghvendra5688/actions/runs/37107125601"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0-11",
      "date": "2026-10-03T07:44:58.000Z",
      "arch": "x86_64",
      "commit": "80c5df56a560c2f044dc968bc733d39a306fea8c",
      "fileid": "https://r2.ropensci.org/720a6585695b651050d211f17a02909d36c488524f209730e2bf57865cd92e4b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/raghvendra5688/actions/runs/37107125601"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0-11",
      "date": "2026-10-03T07:44:48.000Z",
      "arch": "x86_64",
      "commit": "80c5df56a560c2f044dc968bc733d39a306fea8c",
      "fileid": "https://r2.ropensci.org/8b87cd5582229be6e83d0d1294a66f5eeec01894700eaf69d3d18af58630de64",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/raghvendra5688/actions/runs/37107125601"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.0-11",
      "date": "2026-10-03T07:48:25.000Z",
      "arch": "aarch64",
      "commit": "80c5df56a560c2f044dc968bc733d39a306fea8c",
      "fileid": "https://r2.ropensci.org/425a8b943647411399b8d1df44e7903b16fa2b39eca29f12227462a79975a240",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/raghvendra5688/actions/runs/37107125601"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.0-11",
      "date": "2026-10-03T07:44:55.000Z",
      "arch": "x86_64",
      "commit": "80c5df56a560c2f044dc968bc733d39a306fea8c",
      "fileid": "https://r2.ropensci.org/4760488431ecf767c0cd1005adf0446a7003028c21eec3a74f2722bb107156a3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/raghvendra5688/actions/runs/37107125601"
    }
  ]
}