{
  "_id": "6adc9ca658000136b5c840e4",
  "Package": "distinct",
  "Type": "Package",
  "Title": "distinct: a method for differential analyses via hierarchical\npermutation tests",
  "Version": "1.25.2",
  "Author": "Simone Tiberi [aut, cre].",
  "Maintainer": "Simone Tiberi <simone.tiberi@unibo.it>",
  "Description": "distinct is a statistical method to perform differential\ntesting between two or more groups of distributions;\ndifferential testing is performed via hierarchical\nnon-parametric permutation tests on the cumulative distribution\nfunctions (cdfs) of each sample. While most methods for\ndifferential expression target differences in the mean\nabundance between conditions, distinct, by comparing full cdfs,\nidentifies, both, differential patterns involving changes in\nthe mean, as well as more subtle variations that do not involve\nthe mean (e.g., unimodal vs. bi-modal distributions with the\nsame mean). distinct is a general and flexible tool: due to its\nfully non-parametric nature, which makes no assumptions on how\nthe data was generated, it can be applied to a variety of\ndatasets. It is particularly suitable to perform differential\nstate analyses on single cell data (i.e., differential analyses\nwithin sub-populations of cells), such as single cell RNA\nsequencing (scRNA-seq) and high-dimensional flow or mass\ncytometry (HDCyto) data. To use distinct one needs data from\ntwo or more groups of samples (i.e., experimental conditions),\nwith at least 2 samples (i.e., biological replicates) per\ngroup.",
  "biocViews": "Genetics, RNASeq, Sequencing, DifferentialExpression,\nGeneExpression, MultipleComparison, Software, Transcription,\nStatisticalMethod, Visualization, SingleCell, FlowCytometry,\nGeneTarget",
  "License": "GPL (>= 3)",
  "SystemRequirements": "C++17",
  "VignetteBuilder": "knitr",
  "ByteCompile": "true",
  "URL": "https://github.com/SimoneTiberi/distinct",
  "BugReports": "https://github.com/SimoneTiberi/distinct/issues",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-09-24 09:57:02 UTC",
  "RemoteUrl": "https://github.com/bioc/distinct",
  "RemoteRef": "HEAD",
  "RemoteSha": "7ec08672fd2177c33c85779a82ab12deb8232802",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-24 11:40:59 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "distinct_1.25.2.tar.gz",
  "_fileid": "https://r2.ropensci.org/223a96ab7a10a90b7cb7de9da32b507d180c4c91d6f9e407c2bff68bed99bb06",
  "_filesize": 1813545,
  "_sha256": "223a96ab7a10a90b7cb7de9da32b507d180c4c91d6f9e407c2bff68bed99bb06",
  "_expires": "2027-02-01T11:55:16.000Z",
  "_created": "2026-10-24T11:40:59.000Z",
  "_published": "2026-10-24T11:55:18.555Z",
  "_upstream": "https://github.com/bioc/distinct",
  "_status": "success",
  "_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
  },
  "_jobs": [
    {
      "job": 120863308211,
      "time": 355,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "12559425420"
    },
    {
      "job": 120863308286,
      "time": 358,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "12558489988"
    },
    {
      "job": 120863308320,
      "time": 523,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "12558878907"
    },
    {
      "job": 120863308361,
      "time": 434,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12559127824"
    },
    {
      "job": 120863308267,
      "time": 690,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12559053594"
    },
    {
      "job": 120863308317,
      "time": 393,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "12559172837"
    },
    {
      "job": 120863308262,
      "time": 480,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "12559043222"
    },
    {
      "job": 120863308293,
      "time": 350,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12559560477"
    },
    {
      "job": 120863308281,
      "time": 737,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12559166981"
    },
    {
      "job": 120861447980,
      "time": 578,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12558846913"
    },
    {
      "job": 120863308315,
      "time": 300,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12559296572"
    },
    {
      "job": 120863308441,
      "time": 484,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "12558692733"
    },
    {
      "job": 120863308311,
      "time": 384,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "12558872371"
    },
    {
      "job": 120863308342,
      "time": 280,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "12558744090"
    },
    {
      "job": 120863308382,
      "time": 518,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12558769237"
    },
    {
      "job": 120863308345,
      "time": 501,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12559033409"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 1,
    "note": 8
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/40090282369",
  "_commit": {
    "id": "7ec08672fd2177c33c85779a82ab12deb8232802",
    "author": "Simone Tiberi <simone.tiberi@unibo.it>",
    "committer": "Simone Tiberi <simone.tiberi@unibo.it>",
    "message": "T_obs added in results\n",
    "time": 1790243822
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.3",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "doRNG",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "scater",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "UpSetR",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    },
    {
      "week": "2026-30",
      "n": 1
    },
    {
      "week": "2026-39",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.25.2",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.24.2",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "genetics",
    "rnaseq",
    "sequencing",
    "differentialexpression",
    "geneexpression",
    "multiplecomparison",
    "software",
    "transcription",
    "statisticalmethod",
    "visualization",
    "singlecell",
    "flowcytometry",
    "genetarget",
    "openblas",
    "cpp"
  ],
  "_stars": 15,
  "_contributors": [
    {
      "user": "nturaga",
      "count": 8,
      "uuid": 2746443
    },
    {
      "user": "simonetiberi",
      "count": 6,
      "uuid": 24696388
    },
    {
      "user": "hpages",
      "count": 1,
      "uuid": 8810451
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 479,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 676,
    "source": "https://www.bioconductor.org/packages/stats/bioc/distinct"
  },
  "_devurl": "https://github.com/simonetiberi/distinct",
  "_searchresults": 47,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/distinct.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/simonetiberi/distinct",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "distinct_test",
    "log2_FC",
    "plot_cdfs",
    "plot_densities",
    "top_results"
  ],
  "_datasets": [
    {
      "name": "Kang_subset",
      "title": "Subset from the 'Kang18_8vs8()' object of the 'muscData' package.",
      "object": "Kang_subset",
      "file": "Kang_subset.RData",
      "class": [
        "SingleCellExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "res",
      "title": "Results from 'distinct_test' function",
      "object": "res",
      "file": "res.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "gene",
        "cluster_id",
        "p_val",
        "p_adj.loc",
        "p_adj.glb",
        "filtered"
      ],
      "rows": 800,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "distinct-package",
      "title": "distinct: a method for differential analyses via hierarchical permutation tests",
      "topics": [
        "distinct-package",
        "distinct"
      ]
    },
    {
      "page": "distinct_test",
      "title": "Test for differential state between two groups of samples, based on scRNA-seq data.",
      "topics": [
        "distinct_test"
      ]
    },
    {
      "page": "Kang_subset",
      "title": "Subset from the `Kang18_8vs8()` object of the 'muscData' package.",
      "topics": [
        "Kang_subset"
      ]
    },
    {
      "page": "log2_FC",
      "title": "Compute FCs and log2-FCs.",
      "topics": [
        "log2_FC"
      ]
    },
    {
      "page": "plot_cdfs",
      "title": "Plot sample-specific CDFs.",
      "topics": [
        "plot_cdfs"
      ]
    },
    {
      "page": "plot_densities",
      "title": "Plot sample-specific densities.",
      "topics": [
        "plot_densities"
      ]
    },
    {
      "page": "res",
      "title": "Results from 'distinct_test' function",
      "topics": [
        "res"
      ]
    },
    {
      "page": "top_results",
      "title": "Filter significant results.",
      "topics": [
        "top_results"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/distinct/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "assorthead",
    "beachmat",
    "beeswarm",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocNeighbors",
    "BiocParallel",
    "BiocSingular",
    "cli",
    "codetools",
    "cpp11",
    "DelayedArray",
    "digest",
    "doParallel",
    "doRNG",
    "dqrng",
    "farver",
    "FNN",
    "foreach",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggbeeswarm",
    "ggplot2",
    "ggrepel",
    "glue",
    "gridExtra",
    "gtable",
    "IRanges",
    "irlba",
    "isoband",
    "iterators",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "pheatmap",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppAnnoy",
    "RcppArmadillo",
    "RcppEigen",
    "RcppML",
    "RcppProgress",
    "rlang",
    "rngtools",
    "RSpectra",
    "rsvd",
    "Rtsne",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "ScaledMatrix",
    "scales",
    "scater",
    "scuttle",
    "Seqinfo",
    "SingleCellExperiment",
    "sitmo",
    "snow",
    "SparseArray",
    "statmod",
    "SummarizedExperiment",
    "uwot",
    "vctrs",
    "vipor",
    "viridis",
    "viridisLite",
    "withr",
    "XVector"
  ],
  "_sysdeps": [
    {
      "shlib": "liblapack",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.32+ds-5",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libblas",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.32+ds-5",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "distinct.Rmd",
      "filename": "distinct.html",
      "title": "distinct: a method for differential analyses via hierarchical permutation tests",
      "author": "Simone Tiberi",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Bioconductor installation",
        "Differential State analysis",
        "Input data",
        "Differential analyses within sub-populations of cells",
        "Handling covariates and batch effects",
        "Visualizing results",
        "Plotting significant results",
        "Session info"
      ],
      "created": "2020-04-03 11:43:40",
      "modified": "2026-07-21 11:26:14",
      "commits": 11
    }
  ],
  "_score": 6.927370363039024,
  "_indexed": true,
  "_nocasepkg": "distinct",
  "_universes": [
    "bioc",
    "simonetiberi"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.25.2",
      "date": "2026-10-24T11:44:48.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "7ec08672fd2177c33c85779a82ab12deb8232802",
      "fileid": "https://r2.ropensci.org/3c2ff691c97ce26a3f04b1674661fe18c203362aa6841a8ba936727930d3f4aa",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40090282369"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.25.2",
      "date": "2026-10-24T11:46:16.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "7ec08672fd2177c33c85779a82ab12deb8232802",
      "fileid": "https://r2.ropensci.org/bae791ffd1c1ba77149647bbdb065afe8836b0042bab3ca5187a46e7ceb47630",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40090282369"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.25.2",
      "date": "2026-10-24T11:46:05.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "7ec08672fd2177c33c85779a82ab12deb8232802",
      "fileid": "https://r2.ropensci.org/59a14f600a2d782d730ada74f2f5bacab522a88ea12dfc99b5978e47c10b8929",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40090282369"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.25.2",
      "date": "2026-10-24T11:49:06.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "7ec08672fd2177c33c85779a82ab12deb8232802",
      "fileid": "https://r2.ropensci.org/6c82434356bc5967f0fdc99a414024ad8a24392a98e4f37a4c541e18b75e5094",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40090282369"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.25.2",
      "date": "2026-10-24T11:47:34.000Z",
      "arch": "aarch64",
      "commit": "7ec08672fd2177c33c85779a82ab12deb8232802",
      "fileid": "https://r2.ropensci.org/251a5d05d81f03d72a1c5ea1c3e7df5fc78ad259935ccb7a1dc1d72014e8f76c",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40090282369"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.25.2",
      "date": "2026-10-24T11:44:25.000Z",
      "arch": "x86_64",
      "commit": "7ec08672fd2177c33c85779a82ab12deb8232802",
      "fileid": "https://r2.ropensci.org/1361f632304292fae4683a0b8380adc4e8bc8ade5c00be4b54ae2b64ffaee382",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40090282369"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.25.2",
      "date": "2026-10-24T11:47:26.000Z",
      "arch": "aarch64",
      "commit": "7ec08672fd2177c33c85779a82ab12deb8232802",
      "fileid": "https://r2.ropensci.org/fa4bd44c07eaeafa16681772dba9c9c91a1c36cb06e208b0f21a54c2ab334df9",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40090282369"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.25.2",
      "date": "2026-10-24T11:46:17.000Z",
      "arch": "x86_64",
      "commit": "7ec08672fd2177c33c85779a82ab12deb8232802",
      "fileid": "https://r2.ropensci.org/7732d80f6d5c593eeb361e231f2e598666aa5165b3f1aec7a3528f4396b2e544",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40090282369"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.25.2",
      "date": "2026-10-24T11:46:35.000Z",
      "arch": "emscripten",
      "commit": "7ec08672fd2177c33c85779a82ab12deb8232802",
      "fileid": "https://r2.ropensci.org/1467a312898aa15c1a49d9ea8f5061ef06ff9b803d1f86bd16cc338aea8470eb",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40090282369"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.25.2",
      "date": "2026-10-24T11:45:11.000Z",
      "arch": "aarch64",
      "commit": "7ec08672fd2177c33c85779a82ab12deb8232802",
      "fileid": "https://r2.ropensci.org/d98273244299ca4df5d69c3bdc1000420f27e732f892e3f6c0f026864519a634",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40090282369"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.25.2",
      "date": "2026-10-24T11:43:11.000Z",
      "arch": "x86_64",
      "commit": "7ec08672fd2177c33c85779a82ab12deb8232802",
      "fileid": "https://r2.ropensci.org/eb37a9636309ab715bc9297ba3217f0534e8bcc5812d982e97881eb765446d38",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40090282369"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.25.2",
      "date": "2026-10-24T11:43:22.000Z",
      "arch": "x86_64",
      "commit": "7ec08672fd2177c33c85779a82ab12deb8232802",
      "fileid": "https://r2.ropensci.org/721bbc6de87366ecc97309066d61f9bd2609f20238314f029d67097ca34ff2fd",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40090282369"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.25.2",
      "date": "2026-10-24T11:45:59.000Z",
      "arch": "aarch64",
      "commit": "7ec08672fd2177c33c85779a82ab12deb8232802",
      "fileid": "https://r2.ropensci.org/2be54def9873b3827a856587a7f62c5bdf9c19843b281406ba137989444540b5",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40090282369"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.25.2",
      "date": "2026-10-24T11:46:04.000Z",
      "arch": "x86_64",
      "commit": "7ec08672fd2177c33c85779a82ab12deb8232802",
      "fileid": "https://r2.ropensci.org/37fa760b430b291d461048b51e970f47bae3f5571300fd3c02a3a64b4f447cb4",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/40090282369"
    }
  ]
}