{
  "_id": "6a2fade23efcd9bda4327e9d",
  "Package": "BANDITS",
  "Type": "Package",
  "Title": "BANDITS: Bayesian ANalysis of DIfferenTial Splicing",
  "Version": "1.28.0",
  "Author": "Simone Tiberi [aut, cre].",
  "Maintainer": "Simone Tiberi <simone.tiberi@unibo.it>",
  "Description": "BANDITS is a Bayesian hierarchical model for detecting\ndifferential splicing of genes and transcripts, via\ndifferential transcript usage (DTU), between two or more\nconditions. The method uses a Bayesian hierarchical framework,\nwhich allows for sample specific proportions in a\nDirichlet-Multinomial model, and samples the allocation of\nfragments to the transcripts. Parameters are inferred via\nMarkov chain Monte Carlo (MCMC) techniques and a DTU test is\nperformed via a multivariate Wald test on the posterior\ndensities for the average relative abundance of transcripts.",
  "biocViews": "DifferentialSplicing, AlternativeSplicing, Bayesian,\nGenetics, RNASeq, Sequencing, DifferentialExpression,\nGeneExpression, MultipleComparison, Software, Transcription,\nStatisticalMethod, Visualization",
  "License": "GPL (>= 3)",
  "SystemRequirements": "C++17",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.2",
  "ByteCompile": "true",
  "URL": "https://github.com/SimoneTiberi/BANDITS",
  "BugReports": "https://github.com/SimoneTiberi/BANDITS/issues",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:50:01 UTC",
  "RemoteUrl": "https://github.com/bioc/BANDITS",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "b3e67fc7489e96221dc585a7e51a96fb09fe1e0d",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-15 07:39:46 UTC",
    "User": "root"
  },
  "MD5sum": "2a8ff759043869cf0ed08267ef5536ab",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "BANDITS_1.28.0.tar.gz",
  "_fileid": "c7635a5c2c59f4d583374d9f11bc8be6cfe291bc5e7fe87177fcfa77fcf51932",
  "_filesize": 1250131,
  "_sha256": "c7635a5c2c59f4d583374d9f11bc8be6cfe291bc5e7fe87177fcfa77fcf51932",
  "_created": "2026-06-15T07:39:46.000Z",
  "_published": "2026-06-15T07:46:42.780Z",
  "_jobs": [
    {
      "job": 81370138555,
      "time": 208,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7631853567"
    },
    {
      "job": 81370138640,
      "time": 288,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7631877887"
    },
    {
      "job": 81370138635,
      "time": 346,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7631899558"
    },
    {
      "job": 81370138731,
      "time": 293,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7631879322"
    },
    {
      "job": 81370138633,
      "time": 342,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7631898072"
    },
    {
      "job": 81370138697,
      "time": 196,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7631847296"
    },
    {
      "job": 81370138672,
      "time": 325,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7631890477"
    },
    {
      "job": 81370138705,
      "time": 196,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7631847235"
    },
    {
      "job": 81370138708,
      "time": 303,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7631883053"
    },
    {
      "job": 81369193006,
      "time": 359,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7631785142"
    },
    {
      "job": 81370138559,
      "time": 189,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7631845324"
    },
    {
      "job": 81370138588,
      "time": 312,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7631887511"
    },
    {
      "job": 81370138564,
      "time": 216,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7631853843"
    },
    {
      "job": 81370138604,
      "time": 239,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7631861318"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 1,
    "note": 7
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27531108191",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/BANDITS",
  "_commit": {
    "id": "b3e67fc7489e96221dc585a7e51a96fb09fe1e0d",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777380601
  },
  "_maintainer": {
    "name": "Simone Tiberi",
    "email": "simone.tiberi@unibo.it",
    "login": "simonetiberi",
    "twitter": "@tiberi_simone",
    "description": "Associate Professor, Department of Statistical Sciences, University of Bologna.\nStatistician developing computational methods for analyzing omics data.",
    "uuid": 24696388
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.3.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "doRNG",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "R.utils",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "DRIMSeq",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "tximport",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "GenomicFeatures",
      "role": "Suggests"
    },
    {
      "package": "Biostrings",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-40",
      "n": 1
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.29.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.28.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "differentialsplicing",
    "alternativesplicing",
    "bayesian",
    "genetics",
    "rnaseq",
    "sequencing",
    "differentialexpression",
    "geneexpression",
    "multiplecomparison",
    "software",
    "transcription",
    "statisticalmethod",
    "visualization",
    "openblas",
    "cpp"
  ],
  "_stars": 19,
  "_contributors": [
    {
      "user": "nturaga",
      "count": 6,
      "uuid": 2746443
    },
    {
      "user": "simonetiberi",
      "count": 1,
      "uuid": 24696388
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 440,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 512,
    "source": "https://www.bioconductor.org/packages/stats/bioc/BANDITS"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/simonetiberi/bandits",
  "_searchresults": 15,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/BANDITS.html",
    "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",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/simonetiberi/bandits",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "convergence",
    "create_data",
    "eff_len_compute",
    "filter_genes",
    "filter_transcripts",
    "gene",
    "plot_precision",
    "plot_proportions",
    "prior_precision",
    "show",
    "test_DTU",
    "top_genes",
    "top_transcripts",
    "transcript"
  ],
  "_datasets": [
    {
      "name": "gene_tr_id",
      "title": "Gene-transcript matching",
      "object": "gene_tr_id",
      "file": "gene_tr_id.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "gene_id",
        "transcript_id"
      ],
      "rows": 1373,
      "table": true,
      "tojson": true
    },
    {
      "name": "input_data",
      "title": "A 'BANDITS_data' object, generated with 'create_data'",
      "object": "input_data",
      "file": "input_data.RData",
      "class": [
        "BANDITS_data"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "precision",
      "title": "Estimates for the log-precision parameter, generated with 'prior_precision'",
      "object": "precision",
      "file": "precision.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "results",
      "title": "Results of the DTU test, generated with 'test_DTU'",
      "object": "results",
      "file": "results.RData",
      "class": [
        "BANDITS_test"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "BANDITS-package",
      "title": "BANDITS: Bayesian ANalysis of DIfferenTial Splicing",
      "topics": [
        "BANDITS-package",
        "BANDITS"
      ]
    },
    {
      "page": "BANDITS_data-class",
      "title": "BANDITS_data class",
      "topics": [
        "BANDITS_data",
        "BANDITS_data-class",
        "show,BANDITS_data-method"
      ]
    },
    {
      "page": "BANDITS_test-class",
      "title": "BANDITS_test class",
      "topics": [
        "BANDITS_test",
        "BANDITS_test-class",
        "convergence",
        "convergence,BANDITS_test-method",
        "gene",
        "gene,BANDITS_test-method",
        "plot_proportions",
        "plot_proportions,BANDITS_test-method",
        "show,BANDITS_test-method",
        "top_genes",
        "top_genes,BANDITS_test-method",
        "top_transcripts",
        "top_transcripts,BANDITS_test-method",
        "transcript",
        "transcript,BANDITS_test-method"
      ]
    },
    {
      "page": "create_data",
      "title": "Create a 'BANDITS_data' object",
      "topics": [
        "create_data"
      ]
    },
    {
      "page": "eff_len_compute",
      "title": "Compute the median effective length of transcripts.",
      "topics": [
        "eff_len_compute"
      ]
    },
    {
      "page": "filter_genes",
      "title": "Filter lowly abundant genes.",
      "topics": [
        "filter_genes"
      ]
    },
    {
      "page": "filter_transcripts",
      "title": "Filter lowly abundant transcripts.",
      "topics": [
        "filter_transcripts"
      ]
    },
    {
      "page": "gene_tr_id",
      "title": "Gene-transcript matching",
      "topics": [
        "gene_tr_id"
      ]
    },
    {
      "page": "input_data",
      "title": "A 'BANDITS_data' object, generated with 'create_data'",
      "topics": [
        "input_data"
      ]
    },
    {
      "page": "plot_precision",
      "title": "Plot the log-precision estimates",
      "topics": [
        "plot_precision"
      ]
    },
    {
      "page": "precision",
      "title": "Estimates for the log-precision parameter, generated with 'prior_precision'",
      "topics": [
        "precision"
      ]
    },
    {
      "page": "prior_precision",
      "title": "Infer an informative prior for the precision",
      "topics": [
        "prior_precision"
      ]
    },
    {
      "page": "results",
      "title": "Results of the DTU test, generated with 'test_DTU'",
      "topics": [
        "results"
      ]
    },
    {
      "page": "test_DTU",
      "title": "Perform differential splicing",
      "topics": [
        "test_DTU"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/BANDITS/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "BH",
    "BiocGenerics",
    "BiocParallel",
    "cli",
    "codetools",
    "cpp11",
    "data.table",
    "digest",
    "doParallel",
    "doRNG",
    "DRIMSeq",
    "edgeR",
    "farver",
    "foreach",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "IRanges",
    "isoband",
    "iterators",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "locfit",
    "magrittr",
    "MASS",
    "plyr",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "reshape2",
    "rlang",
    "rngtools",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "snow",
    "statmod",
    "stringi",
    "stringr",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_sysdeps": [
    {
      "shlib": "liblapack",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.26+ds-1ubuntu0.1",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libblas",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.26+ds-1ubuntu0.1",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "BANDITS.Rmd",
      "filename": "BANDITS.html",
      "title": "BANDITS: Bayesian ANalysis of DIfferenTial Splicing",
      "author": "Simone Tiberi",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Bioconductor installation",
        "Devel installation from github",
        "Aligning reads",
        "Gene-transcript matching",
        "DTU pipeline",
        "Preliminary information",
        "Optional (recommended): transcript pre-filtering",
        "Load the data",
        "salmon input",
        "kallisto input",
        "Optional (recommended): infer an informative prior for the precision parameter",
        "Test for DTU",
        "Results in detail",
        "Gene level results",
        "Transcript level results",
        "Inference with 3 or more groups",
        "Inference with 1 group only",
        "Session info",
        "References"
      ],
      "created": "2019-04-01 10:27:51",
      "modified": "2025-09-29 14:10:00",
      "commits": 22
    }
  ],
  "_score": 6.108057373783854,
  "_indexed": false,
  "_nocasepkg": "bandits",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/BANDITS",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.28.0",
      "date": "2026-06-15T07:43:27.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "b3e67fc7489e96221dc585a7e51a96fb09fe1e0d",
      "fileid": "840ec41ccdcf3dca7139229f22656a1fbca2d948f102c5bf6361b9e08d06a0f0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27531108191"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.28.0",
      "date": "2026-06-15T07:44:18.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "b3e67fc7489e96221dc585a7e51a96fb09fe1e0d",
      "fileid": "6498b613a2d35d9a260eb0ef971845d23b00aa5c2d3a6125f542995938867a34",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27531108191"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.28.0",
      "date": "2026-06-15T07:43:28.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "b3e67fc7489e96221dc585a7e51a96fb09fe1e0d",
      "fileid": "01c5bb56abab9b6588939efbd8c037ad86bbe1b497e718483d48a8d1998c930f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27531108191"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.28.0",
      "date": "2026-06-15T07:44:18.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "b3e67fc7489e96221dc585a7e51a96fb09fe1e0d",
      "fileid": "c239b91787df36bcabfc122c0f2070f84d371e8b0a381345e8e5b558fb567fa7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27531108191"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.28.0",
      "date": "2026-06-15T07:42:01.000Z",
      "arch": "aarch64",
      "commit": "b3e67fc7489e96221dc585a7e51a96fb09fe1e0d",
      "fileid": "062ae6b5f078b34b76ce4e0eefdd65177a5daf9dc031c3ce47915d7c07b86822",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27531108191"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.28.0",
      "date": "2026-06-15T07:42:53.000Z",
      "arch": "x86_64",
      "commit": "b3e67fc7489e96221dc585a7e51a96fb09fe1e0d",
      "fileid": "f3c37272b6078f6311c8331361c11dba3630fedd30114e09ff5ef9308c4e2141",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27531108191"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.28.0",
      "date": "2026-06-15T07:41:56.000Z",
      "arch": "aarch64",
      "commit": "b3e67fc7489e96221dc585a7e51a96fb09fe1e0d",
      "fileid": "e0b8239ed2e870d49215d9a83115665a6c25c915f51e7504252ddf49f8b2e53e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27531108191"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.28.0",
      "date": "2026-06-15T07:42:49.000Z",
      "arch": "x86_64",
      "commit": "b3e67fc7489e96221dc585a7e51a96fb09fe1e0d",
      "fileid": "a26b9a436acfdf9b8884a314ffd3573692e8283267c2eec4664b4b960aa0b5e9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27531108191"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.28.0",
      "date": "2026-06-15T07:43:21.000Z",
      "arch": "emscripten",
      "commit": "b3e67fc7489e96221dc585a7e51a96fb09fe1e0d",
      "fileid": "2a71f6d5920d09e6f5afe88e5925c13f1cba9977eabb8c35eff4cb973001eec2",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27531108191"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.28.0",
      "date": "2026-06-15T07:42:57.000Z",
      "arch": "x86_64",
      "commit": "b3e67fc7489e96221dc585a7e51a96fb09fe1e0d",
      "fileid": "5b4cc9f96e2b12767cecd3a15d4feea61ad4966241903dc1429d85a40b09924f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27531108191"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.28.0",
      "date": "2026-06-15T07:41:55.000Z",
      "arch": "x86_64",
      "commit": "b3e67fc7489e96221dc585a7e51a96fb09fe1e0d",
      "fileid": "bba4101fed5736cea4906e71510613c6ff7fbf736e779e0be6c4d090ac8c23ae",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27531108191"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.28.0",
      "date": "2026-06-15T07:41:50.000Z",
      "arch": "x86_64",
      "commit": "b3e67fc7489e96221dc585a7e51a96fb09fe1e0d",
      "fileid": "861c7a11ce41eba7bd361f44e1aee192be1ce63d857e4bf7a47ef1c863de4acb",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27531108191"
    }
  ]
}