{
  "_id": "6a5a799109eb0996dd690dbf",
  "Package": "BBNI",
  "Title": "Bayesian Inference of Boolean Genetic Networks",
  "Version": "0.2.0",
  "Authors@R": "c(\nperson(given = \"Anson\", family = \"Li\",\nemail = \"liyuanrui618@gmail.com\",\nrole = c(\"aut\", \"cre\")),\nperson(given = \"Shengtong\", family = \"Han\",\nemail = \"shengtong.han@marquette.edu\",\nrole = \"aut\")\n)",
  "Description": "Implements a fully Bayesian Markov chain Monte Carlo\n(MCMC) approach for inferring the topology and Boolean logic\ntransition functions of gene regulatory networks from noisy,\nbinary time-series expression data. Network structure and\nBoolean rules are sampled jointly from their posterior\ndistribution, providing principled uncertainty quantification\nrather than a single point estimate. Method described in Han et\nal. (2014) <doi:10.1371/journal.pone.0115806>.",
  "License": "BSD_3_clause + file LICENSE",
  "URL": "https://anson-li8.github.io/BBNI/,\nhttps://github.com/anson-li8/BBNI",
  "BugReports": "https://github.com/anson-li8/BBNI/issues",
  "Encoding": "UTF-8",
  "Language": "en-US",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "8.0.0",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "LazyData": "true",
  "Config/pak/sysreqs": "libglpk-dev libxml2-dev",
  "Repository": "https://anson-li8.r-universe.dev",
  "Date/Publication": "2026-07-17 18:29:11 UTC",
  "RemoteUrl": "https://github.com/anson-li8/bbni",
  "RemoteRef": "HEAD",
  "RemoteSha": "319dcacd5cbc815730fe96e7c0f0a3e66ed39700",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-17 18:47:52 UTC",
    "User": "root"
  },
  "Author": "Anson Li [aut, cre],\nShengtong Han [aut]",
  "Maintainer": "Anson Li <liyuanrui618@gmail.com>",
  "_user": "anson-li8",
  "_type": "src",
  "_file": "BBNI_0.2.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/fca3cde8b0af9f04e3f8aecc2177c31be9a05cdca177b8e2470fef9d22b5001f",
  "_filesize": 215690,
  "_sha256": "fca3cde8b0af9f04e3f8aecc2177c31be9a05cdca177b8e2470fef9d22b5001f",
  "_expires": "2026-10-25T18:50:55.000Z",
  "_created": "2026-07-17T18:47:52.000Z",
  "_published": "2026-07-17T18:50:56.757Z",
  "_jobs": [
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      "config": "linux-devel-x86_64",
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  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/anson-li8/actions/runs/29604927989",
  "_status": "success",
  "_upstream": "https://github.com/anson-li8/bbni",
  "_commit": {
    "id": "319dcacd5cbc815730fe96e7c0f0a3e66ed39700",
    "author": "Anson Li <liyuanrui618@gmail.com>",
    "committer": "Anson Li <liyuanrui618@gmail.com>",
    "message": "Bump version to 0.2.0\n",
    "time": 1784312951
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    "email": "liyuanrui618@gmail.com",
    "login": "anson-li8",
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    "uuid": 273617837
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  "_updates": [
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  "_tags": [
    {
      "name": "v0.1.0",
      "date": "2026-06-20"
    },
    {
      "name": "v0.1.1",
      "date": "2026-07-06"
    },
    {
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      "date": "2026-07-17"
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/BBNI"
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  "_pkgdown": "https://anson-li8.github.io/BBNI/",
  "_searchresults": 5,
  "_rbuild": "4.6.1",
  "_assets": [
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    "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",
    "LICENSE",
    "manual.pdf"
  ],
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  "_realowner": "anson-li8",
  "_cranurl": true,
  "_releases": [
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      "date": "2026-07-15"
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  "_exports": [
    "GenerateNetwork",
    "GenerateSample",
    "plot_bbni",
    "plot_network",
    "plot_trace",
    "run_bbni"
  ],
  "_datasets": [
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      "name": "yeast_data",
      "title": "Yeast Cell-Cycle Gene Expression Data",
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        "array"
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        "Heat_Shock_000_minutes__hs-2...8",
        "Heat_Shock_000_minutes__hs-2...9",
        "Heat_Shock_005_minutes__hs-2",
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        "37C_to_25C_shock_-_90_min",
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        "\"heat_shock_25_to_37,_20_minutes\"",
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        "29C_to_33C_-_30_minutes",
        "33C_vs._30C_-_90_minutes",
        "29C_+1M_sorbitol_to_33C_+_1M_sorbitol_-_5_minutes",
        "29C_+1M_sorbitol_to_33C_+_1M_sorbitol_-_15_minutes",
        "29C_+1M_sorbitol_to_33C_+_1M_sorbitol_-_30_minutes",
        "29C_+1M_sorbitol_to_33C_+_*NO_sorbitol_-_5_minutes",
        "29C_+1M_sorbitol_to_33C_+_*NO_sorbitol_-_15_minutes",
        "29C_+1M_sorbitol_to_33C_+_*NO_sorbitol_-_30_minutes",
        "constant_0.32_mM_H2O2_(40_min)_rescan",
        "constant_0.32_mM_H2O2_(60_min)_redo",
        "constant_0.32_mM_H2O2_(80_min)_redo",
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        "1.5_mM_diamide_(30_min)",
        "1.5_mM_diamide_(40_min)",
        "1.5_mM_diamide_(50_min)",
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        "YPD_stationary_phase_3_d_ypd-1",
        "YPD_stationary_phase_5_d_ypd-1",
        "YPD_stationary_phase_7_d_ypd-1",
        "YPD_stationary_phase_22_d_ypd-1",
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        "DBY7286_37degree_heat_-_20_min",
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        "DBY7286_+_0.3_mM_H2O2_(20_min)",
        "DBYmsn2msn4_(good_strain)_+_0.32_mM_H2O2",
        "DBYmsn2/4_(real_strain)_+_0.32_mM_H2O2_(20_min)",
        "DBYyap1-_+_0.3_mM_H2O2_(20_min)",
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        "Ca_60min_(1)",
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        "Ca+FK_15min_(5)",
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        "Ca/Ca+FK_15min_(2)",
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        "wt/crz1_Ca_15min_(2)",
        "wt/crz1_Ca_30min_(2)",
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        "Na_45min",
        "Na_60min",
        "Na+FK_15min",
        "Na+FK_30min",
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        "Na/Na+FK_45min_(1)",
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        "DES460_+_0.02%_MMS_-_30_min",
        "DES460_+_0.2%_MMS_-_45_min",
        "DES460_+_0.02%_MMS_-_60_min",
        "DES460_+_0.02%_MMS_-_120_min",
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        "DES459_(mec1-)_+_0.02%_MMS_-_30_min",
        "DES459_(mec1-)_+_0.02%_MMS_-_45_min",
        "DES459_(mec1-)_+_0.02%_MMS_-_60_min",
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        "wt_plus_gamma_5_min",
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        "DES460_(wt)_-_mock_irradiation_-_5_min",
        "DES460_(wt)_-_mock_irradiation_-_30_min",
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        "DES460_(wt)_-_mock_irradiation_-_90_min",
        "mec1_plus_gamma_5_min",
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        "mec1_plus_gamma_60_min",
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        "DES459_(mec1)_-_mock_irradiation_-_30_min",
        "DES459_(mec1)_-_mock_irradiation_-_60_min",
        "DES460_(wild_type)_+_heat_20_min",
        "DES459_(mec1)_+_heat_20_min",
        "MHY1_(dun1)_+_heat_20_min",
        "DES460_vs._DES460_YPD_log_phase_control",
        "DES459_(mec1)_-_log_phase_(IR_time_=_0_sample)",
        "DES460(wt)_vs._DES459(mec1)_genomic_DNA_comparison",
        "DES460(wt)_vs._DES459(mec1)_genomic_DNA_comparison_#2",
        "DES460_genomic_DNA_vs._MHY26_(dun1)_genomic_DNA",
        "MHY1_(crt1)_vs._CRY1_(wild_type)_-_log_phase",
        "a_vs._a/a",
        "alpha_vs._alpha/alpha",
        "alpha_vs._a/alpha",
        "alpha/delta_vs._a/alpha_diploid",
        "alpha/delta_vs._a/alpha_-_#2",
        "a/delta_vs._a/alpha_diploid",
        "a/delta_vs._a/alpha_-_#2",
        "NBW7_MgCl2_(1)_50mM",
        "NBW7_MgCl2_(2)_200mM",
        "NBW7_CaCl2_(1)_2mM",
        "NBW7_CaCl2_(2)_10mM",
        "NBW7_CaCl2_200mM_40min",
        "NBW7_CaCl2_200mM_50min",
        "NBW7_Zn_10mM_(1)_15min",
        "NBW7_Zn_10mM_(3)_45min",
        "NBW7_Zn_10mM_(4)_60min",
        "NBW7_Zn_10mM_(5)_120min",
        "NBW7_ZnCl2_(1)_1mM",
        "NBW7_ZnCl2_(2)_3mM",
        "NBW7_ZnCl2_exp1_(1)_1mM",
        "NBW7_ZnCl2_exp1_(3)_6mM",
        "NBW7_ZnCl2_exp1_(4)_10mM",
        "DBY7286_ZnCl2_06mM",
        "DBY7286_ZnCl2_10mM",
        "DBY7286_ZnCl2_exp2_06mM",
        "DBY7286_ZnCl2_exp2_10mM",
        "DBY7286_ZnCl2_exp2_15mM",
        "DBY7286_ZnCl2_Exp3_15mM",
        "DBY7286_ZnCl2_Exp3_20mM",
        "NBW7_CoCl2_1mM",
        "NBW7_CoCl2_exp1_0.5mM",
        "NBW7_CoCl2_exp1_1mM",
        "NBW7_CoCl2_exp1_5mM",
        "NBW7_CoCl2_exp2_0.5mM",
        "NBW7_CoCl2_exp2_1mM",
        "NBW7_CoCl2_exp2_2mM",
        "NBW7_CoCl2_exp2_5mM",
        "DBY7286_CoCl2_1mM",
        "DBY7286_CoCl2_3mM",
        "DBY7286_CoCl2_exp2_1mM",
        "NBW7_MnCl2_3mM_(2)_30min",
        "NBW7_MnCl2_3mM_(3)_45min",
        "NBW7_MnCl2_3mM_(4)_60min",
        "NBW7_MnCl2_3mM_(5)_120min",
        "NBW7_MnCl2_0.3mM",
        "NBW7_MnCl2_1mM",
        "NBW7_MnCl2_exp1_0.5mM",
        "NBW7_MnCl2_exp1_1mM",
        "NBW7_MnCl2_exp1_2mM",
        "NBW7_MnCl2_exp1_3mM",
        "NBW7_MnCl2_exp2_0.5mM",
        "NBW7_MnCl2_exp2_1mM",
        "NBW7_MnCl2_exp2_2mM",
        "NBW7_MnCl2_exp2_3mM",
        "DBY7286_MnCl2_2mM",
        "DBY7286_MnCl2_5mM",
        "DBY7286_MnCl2_Mn_exp2_2mM",
        "DBY7286_MnCl2_Mn_exp2_5mM",
        "NBW7_NiCl2_1mM",
        "NBW7_NiCl2_exp1_0.5mM",
        "NBW7_NiCl2_exp1_1mM",
        "NBW7_NiCl2_exp1_2mM",
        "NBW7_NiCl2_exp1_3mM",
        "DBY7286_NiCl2_1mM",
        "NBW7_CdCl2_exp3_0.05mM",
        "NBW7_CdCl2_exp3_0.1mM",
        "NBW7_CdCl2_exp3_0.2mM",
        "NBW7_CdCl2_Exp4_0.1mM",
        "NBW7_CdCl2_Exp4_0.2mM",
        "NBW7_CdCl2_Exp4_0.4mM",
        "DBY7286_CdCl2_0.1mM",
        "DBY7286_CdCl2_0.2mM",
        "DBY7286_CdCl2_exp2_0.2mM",
        "NBW7_CuCl2_exp1_(1)_0.3mM",
        "NBW7_CuCl2_exp1_(2)_1mM",
        "NBW7_CuCl2_exp1_(3)_3mM",
        "NBW7_CuCl2_exp1_(4)_10mM",
        "DBY7286_CuCl2_3mM",
        "DBY7286_CuCl2_6mM",
        "DBY7286_CuCl2_exp2_3mM",
        "DBY7286_CuCl2_exp2_6mM",
        "NBW7_FeCl2_exp1_0.3mM",
        "NBW7_FeCl2_exp1_1mM",
        "aft1_ZnCl2_6mM",
        "aft1_CoCl2_2mM",
        "aft1_MnCl2_2mM",
        "aft1_NiCl2_2mM_",
        "High_to_Low-Pi_YPAD_of_NBW7_10min",
        "High_to_Low-Pi_YPAD_of_NBW7_20min",
        "High_to_Low-Pi_YPAD_of_NBW7_30min",
        "High_to_Low-Pi_YPAD_of_NBW7_45min",
        "High_to_Low-Pi_YPAD_of_NBW7_60min",
        "NBW7_in_MM_Low-Pi_at_60min",
        "NBW7_MM_Low-_vs_High-Pi",
        "pho4_pho85_vs_WT_in_YPAD",
        "PHO4c_vs._wild_type",
        "pho80_mutant_vs_wild_type",
        "\"PHO81c_vs._wild_type,_exp.1\"",
        "\"PHO81c_vs._wild_type,_exp.2\"",
        "pho85_delete_vs._wild_type",
        "\"pho85_delete_vs._WT,_exp.2\"",
        "pho85_vs._pho4_pho85_double",
        "DY1457_(wild_type)_3_mM_vs._10_uM_zinc_y13-75",
        "DY1457_(wild_type)_3_mM_vs._10_uM_zinc_y12-121",
        "DY1457_(wild_type)_3_mM_vs._61_nM_zinc_y13-121",
        "DY1457_(wild_type)_3_mM_vs._76_nM_zinc_y12-122",
        "DY_zap1_3_mM_vs._10_uM_zinc_#2_y12-123",
        "DY_(zap1)_3_mM_vs._61_nM_zinc_y13-76",
        "DY_zap1_3_mM_vs._76_nM_zinc_y12-124",
        "wt_vs_zap1_-_61_nM_zinc_y13-77",
        "wild_type_vs._zap1_-_76_nM_zinc_y12-125",
        "spo 0",
        "spo 30min",
        "spo 7h",
        "spo 9h",
        "Primig_SK1a/alpha 1h",
        "Primig_SK1a/alpha 2h",
        "Primig_SK1a/alpha 3h",
        "Primig_SK1a/alpha 4h",
        "Primig_SK1a/alpha 6h",
        "Primig_SK1a/alpha 8h",
        "Primig_SK1a/alpha 10h",
        "Primig_SK1alpha/alpha 2h",
        "Primig_SK1alpha/alpha 4h",
        "Primig_SK1alpha/alpha 6h",
        "Primig_SK1alpha/alpha 8h",
        "Primig_W303a/alpha 2h",
        "Primig_W303a/alpha 6h",
        "Primig_W303a/alpha 8h",
        "Primig_W303a/alpha 10h",
        "Primig_W303a/alpha 12h",
        "Primig_W303a/a 2h",
        "Primig_W303a/a 4h",
        "Primig_W303a/a 6h"
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      "rows": 14,
      "table": true,
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    }
  ],
  "_help": [
    {
      "page": "GenerateNetwork",
      "title": "Generate Initial Network Topology",
      "topics": [
        "GenerateNetwork"
      ]
    },
    {
      "page": "GenerateSample",
      "title": "Simulate Boolean Network Observation Dataset",
      "topics": [
        "GenerateSample"
      ]
    },
    {
      "page": "plot_bbni",
      "title": "Plot the Inferred Bayesian Boolean Network",
      "topics": [
        "plot_bbni"
      ]
    },
    {
      "page": "plot_network",
      "title": "Plot a Single Boolean Network",
      "topics": [
        "plot_network"
      ]
    },
    {
      "page": "plot_trace",
      "title": "Plot MCMC Trace for BBNI",
      "topics": [
        "plot_trace"
      ]
    },
    {
      "page": "run_bbni",
      "title": "Execute Metropolis-within-Gibbs MCMC Sampler for Boolean Networks",
      "topics": [
        "run_bbni"
      ]
    },
    {
      "page": "yeast_data",
      "title": "Yeast Cell-Cycle Gene Expression Data",
      "topics": [
        "yeast_data"
      ]
    }
  ],
  "_readme": "https://github.com/anson-li8/bbni/raw/HEAD/README.md",
  "_rundeps": [
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    "cli",
    "cpp11",
    "glue",
    "igraph",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "pkgconfig",
    "rlang",
    "vctrs"
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  "_vignettes": [
    {
      "source": "Introduction_to_BBNI.Rmd",
      "filename": "Introduction_to_BBNI.html",
      "title": "Bayesian Boolean Network Inference with BBNI",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Setup and simulation",
        "Running the MCMC sampler",
        "Analyzing the output",
        "Convergence: trace plot",
        "Final sampled network",
        "Recovery of the true network",
        "Posterior summarization by Bayesian model averaging",
        "Visualizing network recovery",
        "Application to real-world biological data",
        "Next steps",
        "Session information"
      ],
      "created": "2026-06-19 23:00:32",
      "modified": "2026-06-28 01:38:31",
      "commits": 12
    }
  ],
  "_score": 4.3979400086720375,
  "_indexed": true,
  "_nocasepkg": "bbni",
  "_universes": [
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  "_previous": "0.1.1.9000",
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