{
  "_id": "6ae5ec1595ca2370cc8d216b",
  "Package": "presto",
  "Title": "Fast Functions for Differential Expression Using Wilcoxon and\nAUC",
  "Version": "1.1.0",
  "Authors@R": "c(\nperson(\"Ilya\", \"Korsunsky\", email = \"ilya.korsunsky@gmail.com\",\nrole = c(\"aut\"), comment = c(ORCID = \"0000-0003-4848-3948\")),\nperson(\"Aparna\", \"Nathan\",\nrole = \"aut\"),\nperson(\"Nghia\", \"Millard\",\nrole = \"aut\", comment = c(ORCID = \"0000-0002-0518-7674\")),\nperson(\"Soumya\", \"Raychaudhuri\",\nrole = c(\"aut\"), comment = c(ORCID = \"0000-0002-1901-8265\")),\nperson(\"Kamil\", \"Slowikowski\", email = \"kslowikowski@gmail.com\",\nrole = c(\"cre\", \"ctb\"), comment = c(ORCID = \"0000-0002-2843-6370\")),\nperson(\"Austin\", \"Hartman\",\nrole = c(\"ctb\"), comment = c(ORCID = \"0000-0001-7278-1852\"))\n)",
  "Description": "Scalable implementation of the Wilcoxon rank sum test and\nthe area under the receiver operating characteristic curve\n(also known as auROC or AUC) statistic. Interfaces to dense and\nsparse matrices, as well as the genomics analysis frameworks\n'Seurat' and 'SingleCellExperiment'.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.3",
  "NeedsCompilation": "yes",
  "VignetteBuilder": "knitr",
  "Packaged": {
    "Date": "2026-10-31 12:20:47 UTC",
    "User": "root"
  },
  "Author": "Ilya Korsunsky [aut] (ORCID:\n<https://orcid.org/0000-0003-4848-3948>), Aparna Nathan [aut],\nNghia Millard [aut] (ORCID:\n<https://orcid.org/0000-0002-0518-7674>), Soumya Raychaudhuri\n[aut] (ORCID: <https://orcid.org/0000-0002-1901-8265>), Kamil\nSlowikowski [cre, ctb] (ORCID:\n<https://orcid.org/0000-0002-2843-6370>), Austin Hartman [ctb]\n(ORCID: <https://orcid.org/0000-0001-7278-1852>)",
  "Maintainer": "Kamil Slowikowski <kslowikowski@gmail.com>",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://slowkow.r-universe.dev",
  "Date/Publication": "2026-09-30 13:56:03 UTC",
  "RemoteUrl": "https://github.com/cran/presto",
  "RemoteRef": "HEAD",
  "RemoteSha": "5e323fb82db78c8f5b7edbec2c68e20dcb43a9a8",
  "_user": "slowkow",
  "_type": "src",
  "_file": "presto_1.1.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/eee2f28711368264aa43054ac600d673851d6e6eb4e7de6f2c589aa0855f0d4b",
  "_filesize": 214715,
  "_sha256": "eee2f28711368264aa43054ac600d673851d6e6eb4e7de6f2c589aa0855f0d4b",
  "_expires": "2027-02-08T13:24:35.000Z",
  "_created": "2026-10-31T12:20:47.000Z",
  "_published": "2026-10-31T13:24:37.113Z",
  "_upstream": "https://github.com/cran/presto",
  "_status": "success",
  "_maintainer": {
    "name": "Kamil Slowikowski",
    "email": "kslowikowski@gmail.com",
    "login": "slowkow",
    "bluesky": "@slowkow.com",
    "linkedin": "in/kslowikowski",
    "orcid": "0000-0002-2843-6370",
    "description": "Computational biologist. Using transcriptomics to learn about inflammation and cancer.",
    "uuid": 209714
  },
  "_jobs": [
    {
      "job": 124535800494,
      "time": 190,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "13042781243"
    },
    {
      "job": 124535800542,
      "time": 244,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "13042681790"
    },
    {
      "job": 124535800504,
      "time": 176,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "13043080347"
    },
    {
      "job": 124535800482,
      "time": 203,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "13042119246"
    },
    {
      "job": 124535800465,
      "time": 115,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "13043673915"
    },
    {
      "job": 124535800496,
      "time": 546,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "13042338120"
    },
    {
      "job": 124535800471,
      "time": 191,
      "config": "macos-release-arm64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13043577841"
    },
    {
      "job": 124535800481,
      "time": 320,
      "config": "macos-release-x86_64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13042427623"
    },
    {
      "job": 124534971100,
      "time": 231,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "13042203749"
    },
    {
      "job": 124535800410,
      "time": 143,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "13042960494"
    },
    {
      "job": 124535800453,
      "time": 423,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "13043235053"
    },
    {
      "job": 124535800470,
      "time": 185,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "13042626835"
    },
    {
      "job": 124535800565,
      "time": 183,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "13042222689"
    },
    {
      "job": 124535800514,
      "time": 389,
      "config": "windows-release-arm64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13042901232"
    },
    {
      "job": 124535800533,
      "time": 184,
      "config": "windows-release-x86_64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13042691545"
    }
  ],
  "_buildurl": "https://github.com/r-universe/slowkow/actions/runs/41200400499",
  "_commit": {
    "id": "5e323fb82db78c8f5b7edbec2c68e20dcb43a9a8",
    "author": "Kamil Slowikowski <kslowikowski@gmail.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.1.0\n",
    "time": 1790776563
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "Seurat",
      "role": "Suggests"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Suggests"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Suggests"
    },
    {
      "package": "DelayedArray",
      "role": "Suggests"
    },
    {
      "package": "broom",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "DESeq2",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2026-40",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "1.1.0",
      "date": "2026-09-30"
    }
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "slowkow",
      "count": 1,
      "uuid": 209714
    }
  ],
  "_userbio": {
    "uuid": 209714,
    "type": "user",
    "name": "Kamil Slowikowski",
    "followers": 831,
    "description": "Computational biologist. Using transcriptomics to learn about inflammation and cancer."
  },
  "_downloads": {
    "count": 8653,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/presto"
  },
  "_searchresults": 1484,
  "_topics": [
    "cpp"
  ],
  "_abi": {
    "exports": [],
    "imports": [
      {
        "key": "Rcpp::Rcpp_precious_preserve()",
        "hash": "33a97ea62b293da6"
      },
      {
        "key": "Rcpp::Rcpp_precious_remove()",
        "hash": "63d26947ba7e1377"
      },
      {
        "key": "Rcpp::dataptr()",
        "hash": "54e69ad2e6668c83"
      },
      {
        "key": "Rcpp::demangle()",
        "hash": "b0cfd6754c5ebc4e"
      },
      {
        "key": "Rcpp::enterRNGScope()",
        "hash": "a04a299137cef947"
      },
      {
        "key": "Rcpp::exitRNGScope()",
        "hash": "a04a299137cef947"
      },
      {
        "key": "Rcpp::rcpp_get_stack_trace()",
        "hash": "c684a9bbe15cdc52"
      },
      {
        "key": "Rcpp::rcpp_set_stack_trace()",
        "hash": "33a97ea62b293da6"
      }
    ]
  },
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/presto.html",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_realowner": "slowkow",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.1.0",
      "date": "2026-09-30"
    }
  ],
  "_exports": [
    "%>%",
    "collapse_counts",
    "compute_hash",
    "nnzeroGroups",
    "pseudobulk_deseq2",
    "pseudobulk_one_vs_all",
    "pseudobulk_pairwise",
    "pseudobulk_within",
    "rank_matrix",
    "sumGroups",
    "summarize_dge_pairs",
    "top_markers",
    "top_markers_dds",
    "toy_sce",
    "toy_seurat",
    "wilcoxauc"
  ],
  "_help": [
    {
      "page": "collapse_counts",
      "title": "Collapse a single-cell count matrix into pseudobulks",
      "topics": [
        "collapse_counts"
      ]
    },
    {
      "page": "compute_hash",
      "title": "Compute a unique integer hash for each row of a data.frame",
      "topics": [
        "compute_hash"
      ]
    },
    {
      "page": "nnzeroGroups",
      "title": "Group-wise non-zero counts of a matrix along one axis",
      "topics": [
        "nnzeroGroups",
        "nnzeroGroups.dgCMatrix",
        "nnzeroGroups.matrix"
      ]
    },
    {
      "page": "pseudobulk_deseq2",
      "title": "Pseudobulk differential expression with DESeq2",
      "topics": [
        "pseudobulk_deseq2"
      ]
    },
    {
      "page": "pseudobulk_one_vs_all",
      "title": "Pseudobulk DESeq2: one-vs-all contrasts",
      "topics": [
        "pseudobulk_one_vs_all"
      ]
    },
    {
      "page": "pseudobulk_pairwise",
      "title": "Pseudobulk DESeq2: pairwise contrasts",
      "topics": [
        "pseudobulk_pairwise"
      ]
    },
    {
      "page": "pseudobulk_within",
      "title": "Pseudobulk DESeq2: within-group contrasts",
      "topics": [
        "pseudobulk_within"
      ]
    },
    {
      "page": "rank_matrix",
      "title": "Column-wise tied ranks of a matrix",
      "topics": [
        "rank_matrix",
        "rank_matrix.dgCMatrix",
        "rank_matrix.matrix"
      ]
    },
    {
      "page": "sumGroups",
      "title": "Group-wise sum of a matrix along one axis",
      "topics": [
        "sumGroups",
        "sumGroups.dgCMatrix",
        "sumGroups.matrix"
      ]
    },
    {
      "page": "summarize_dge_pairs",
      "title": "Summarize directional pairwise DGE results",
      "topics": [
        "summarize_dge_pairs"
      ]
    },
    {
      "page": "top_markers",
      "title": "Top markers per group from wilcoxauc results",
      "topics": [
        "top_markers"
      ]
    },
    {
      "page": "top_markers_dds",
      "title": "Top markers per group from pseudobulk DESeq2 results",
      "topics": [
        "top_markers_dds"
      ]
    },
    {
      "page": "toy_sce",
      "title": "Toy SingleCellExperiment object for examples and tests",
      "topics": [
        "toy_sce"
      ]
    },
    {
      "page": "toy_seurat",
      "title": "Toy Seurat object for examples and tests",
      "topics": [
        "toy_seurat"
      ]
    },
    {
      "page": "wilcoxauc",
      "title": "Fast Wilcoxon rank-sum test and auROC across groups",
      "topics": [
        "wilcoxauc",
        "wilcoxauc.default",
        "wilcoxauc.Seurat",
        "wilcoxauc.seurat",
        "wilcoxauc.SingleCellExperiment"
      ]
    }
  ],
  "_readme": "https://github.com/cran/presto/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "cpp11",
    "data.table",
    "dplyr",
    "generics",
    "glue",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "Rcpp",
    "RcppArmadillo",
    "rlang",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr"
  ],
  "_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"
    }
  ],
  "_vignettes": [
    {
      "source": "getting-started.Rmd",
      "filename": "getting-started.html",
      "title": "Getting started with presto",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Demo data",
        "Quick start",
        "Result columns",
        "Top markers per cluster",
        "Restricting to a subset of groups",
        "Seurat and SingleCellExperiment",
        "Notes on input types",
        "Session info"
      ],
      "created": "2026-09-30 13:56:03",
      "modified": "2026-09-30 13:56:03",
      "commits": 1
    },
    {
      "source": "pseudobulk.Rmd",
      "filename": "pseudobulk.html",
      "title": "Pseudobulk differential expression with DESeq2",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Why pseudobulk?",
        "Demo data",
        "Step 1: collapse cells to pseudobulks",
        "Step 2: one-vs-all DESeq2",
        "Step 3: top markers per cluster",
        "Step 4: pairwise cluster contrasts",
        "Step 5: within-cluster Case vs Control",
        "Tips",
        "Session info"
      ],
      "created": "2026-09-30 13:56:03",
      "modified": "2026-09-30 13:56:03",
      "commits": 1
    }
  ],
  "_score": 6.585721859377703,
  "_indexed": true,
  "_nocasepkg": "presto",
  "_universes": [
    "slowkow"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-10-31T12:23:23.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "5e323fb82db78c8f5b7edbec2c68e20dcb43a9a8",
      "fileid": "https://r2.ropensci.org/0b157e878a01251ecba77e51eb91187304bfd27dbbd04fb44c21508e22008d09",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/slowkow/actions/runs/41200400499"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-10-31T12:23:53.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "5e323fb82db78c8f5b7edbec2c68e20dcb43a9a8",
      "fileid": "https://r2.ropensci.org/0570c1a3e3dd852926da08fba37ef7d73ddc03cb271597b04a60418efd34291d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/slowkow/actions/runs/41200400499"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-10-31T12:23:14.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "5e323fb82db78c8f5b7edbec2c68e20dcb43a9a8",
      "fileid": "https://r2.ropensci.org/82cd4ebfdcba87c813f6899dcdf4e6e0907e6b562f3e64a3d0c48bd8c82b162b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/slowkow/actions/runs/41200400499"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.1.0",
      "date": "2026-10-31T12:23:31.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "5e323fb82db78c8f5b7edbec2c68e20dcb43a9a8",
      "fileid": "https://r2.ropensci.org/27ff274c7e15f2546080e0e031908d7b8b0d1b0eac9674e20bc08122258a029e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/slowkow/actions/runs/41200400499"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-10-31T13:21:05.000Z",
      "arch": "aarch64",
      "commit": "5e323fb82db78c8f5b7edbec2c68e20dcb43a9a8",
      "fileid": "https://r2.ropensci.org/6e19f4cf476a31e6111bdb81fad914c16ab26f8870e7e26c2a40c5203abb7b26",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/slowkow/actions/runs/41200400499"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-10-31T12:28:33.000Z",
      "arch": "x86_64",
      "commit": "5e323fb82db78c8f5b7edbec2c68e20dcb43a9a8",
      "fileid": "https://r2.ropensci.org/f6cfdef3c6723044436d7365060b963c4933ca5326df905edefd15c42a77cc43",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/slowkow/actions/runs/41200400499"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-10-31T13:22:55.000Z",
      "arch": "aarch64",
      "commit": "5e323fb82db78c8f5b7edbec2c68e20dcb43a9a8",
      "fileid": "https://r2.ropensci.org/0fa252067a52cb08b0d47b6989458d1bc7ebfd27d456f72d05f18e7d2d4b2cb6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/slowkow/actions/runs/41200400499"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "1.1.0",
      "date": "2026-10-31T12:26:35.000Z",
      "arch": "x86_64",
      "commit": "5e323fb82db78c8f5b7edbec2c68e20dcb43a9a8",
      "fileid": "https://r2.ropensci.org/e347136166a2b024023efec892de6488ce78113342b3d71450aeea182dfa74a5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/slowkow/actions/runs/41200400499"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.1.0",
      "date": "2026-10-31T12:23:27.000Z",
      "arch": "emscripten",
      "commit": "5e323fb82db78c8f5b7edbec2c68e20dcb43a9a8",
      "fileid": "https://r2.ropensci.org/a89ec72e71d743ea559a1f59a55d943c57a04b6e067b2be7260afb333cb9fdec",
      "status": "success",
      "buildurl": "https://github.com/r-universe/slowkow/actions/runs/41200400499"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-10-31T12:26:30.000Z",
      "arch": "aarch64",
      "commit": "5e323fb82db78c8f5b7edbec2c68e20dcb43a9a8",
      "fileid": "https://r2.ropensci.org/078ae0de5fba9fb64a887e99da3051ab64f266c6446fa8eb013af14aa03973ae",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/slowkow/actions/runs/41200400499"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-10-31T12:22:12.000Z",
      "arch": "x86_64",
      "commit": "5e323fb82db78c8f5b7edbec2c68e20dcb43a9a8",
      "fileid": "https://r2.ropensci.org/7fc0becedc6c83e3f6c97a85fc5440b83662fbb7e41d8fd26ae9296efcf8b9f5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/slowkow/actions/runs/41200400499"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-10-31T12:22:28.000Z",
      "arch": "x86_64",
      "commit": "5e323fb82db78c8f5b7edbec2c68e20dcb43a9a8",
      "fileid": "https://r2.ropensci.org/e3e346eb269d92065c769195b39bbe36910169007f5a15820deeb589773c501e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/slowkow/actions/runs/41200400499"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-10-31T12:25:47.000Z",
      "arch": "aarch64",
      "commit": "5e323fb82db78c8f5b7edbec2c68e20dcb43a9a8",
      "fileid": "https://r2.ropensci.org/658c212c9e3afbe4c185371bbde760d0b5589e91a015b82f896649c4acf013f9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/slowkow/actions/runs/41200400499"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "1.1.0",
      "date": "2026-10-31T12:22:24.000Z",
      "arch": "x86_64",
      "commit": "5e323fb82db78c8f5b7edbec2c68e20dcb43a9a8",
      "fileid": "https://r2.ropensci.org/5b3a5c6a7b050b0864c2c43d225f748f9de827014978b462f4cea96d7dd35078",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/slowkow/actions/runs/41200400499"
    }
  ]
}