{
  "_id": "6a1afade1d7bb097a09fc7cf",
  "Package": "SEtools",
  "Type": "Package",
  "Title": "SEtools: tools for working with SummarizedExperiment",
  "Version": "1.27.0",
  "Authors@R": "person(\"Pierre-Luc\", \"Germain\", email=\"pierre-luc.germain@hest.ethz.ch\", role=c(\"cre\",\"aut\"), comment=c(ORCID=\"0000-0003-3418-4218\"))",
  "Description": "This includes a set of convenience functions for working\nwith the SummarizedExperiment class. Note that plotting\nfunctions historically in this package have been moved to the\nsechm package (see vignette for details).",
  "biocViews": "GeneExpression",
  "VignetteBuilder": "knitr",
  "License": "GPL",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.2",
  "BugReports": "https://github.com/plger/SEtools",
  "Config/pak/sysreqs": "libicu-dev libpng-dev libxml2-dev libssl-dev perl\nlibnode-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:50:54 UTC",
  "RemoteUrl": "https://github.com/bioc/SEtools",
  "RemoteRef": "HEAD",
  "RemoteSha": "67898208e54f2d58b682dd58d6f64fee3a025670",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:49:46 UTC",
    "User": "root"
  },
  "Author": "Pierre-Luc Germain [cre, aut] (ORCID:\n<https://orcid.org/0000-0003-3418-4218>)",
  "Maintainer": "Pierre-Luc Germain <pierre-luc.germain@hest.ethz.ch>",
  "MD5sum": "af3a0b3abeb31379200cc22971583d9a",
  "_user": "bioc",
  "_type": "src",
  "_file": "SEtools_1.27.0.tar.gz",
  "_fileid": "41a532da72c0d22316e6317219da504111eeed298d021fa989adfa4280d27d0f",
  "_filesize": 446947,
  "_sha256": "41a532da72c0d22316e6317219da504111eeed298d021fa989adfa4280d27d0f",
  "_created": "2026-05-30T09:49:46.000Z",
  "_published": "2026-05-30T14:57:34.751Z",
  "_jobs": [
    {
      "job": 78640772338,
      "time": 208,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7307538685"
    },
    {
      "job": 78640772341,
      "time": 363,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307552981"
    },
    {
      "job": 78640772342,
      "time": 352,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307552629"
    },
    {
      "job": 78640772333,
      "time": 176,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7309049202"
    },
    {
      "job": 78640772332,
      "time": 225,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7309053685"
    },
    {
      "job": 78639977892,
      "time": 244,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307308350"
    },
    {
      "job": 78640772337,
      "time": 134,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307531317"
    },
    {
      "job": 78640772344,
      "time": 342,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307552092"
    },
    {
      "job": 78640772346,
      "time": 280,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307546504"
    },
    {
      "job": 78640772348,
      "time": 281,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307546273"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 1,
    "note": 14
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677092643",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/SEtools",
  "_commit": {
    "id": "67898208e54f2d58b682dd58d6f64fee3a025670",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380654
  },
  "_maintainer": {
    "name": "Pierre-Luc Germain",
    "email": "pierre-luc.germain@hest.ethz.ch",
    "login": "plger",
    "orcid": "0000-0003-3418-4218",
    "description": "like sailors who on the open sea must reconstruct their ship but are never able to start afresh from the bottom...",
    "uuid": 9786697
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Depends"
    },
    {
      "package": "sechm",
      "role": "Depends"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "DESeq2",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "edgeR",
      "role": "Imports"
    },
    {
      "package": "openxlsx",
      "role": "Imports"
    },
    {
      "package": "pheatmap",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "circlize",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "sva",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-29",
      "n": 3
    },
    {
      "week": "2025-30",
      "n": 1
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.27.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.26.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "geneexpression"
  ],
  "_stars": 3,
  "_contributors": [
    {
      "user": "plger",
      "count": 173,
      "uuid": 9786697
    },
    {
      "user": "nturaga",
      "count": 12,
      "uuid": 2746443
    },
    {
      "user": "jwokaty",
      "count": 12,
      "uuid": 1744257
    },
    {
      "user": "hpages",
      "count": 1,
      "uuid": 8810451
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 366,
    "source": "https://www.bioconductor.org/packages/stats/bioc/SEtools"
  },
  "_devurl": "https://github.com/plger/setools",
  "_searchresults": 97,
  "_rbuild": "4.6.0",
  "_assets": [
    "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",
    "extra/SEtools.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/plger/setools",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "aggSE",
    "castSE",
    "flattenPB",
    "log2FC",
    "mergeSEs",
    "resetAllSEtoolsOptions",
    "se2xls",
    "sehm",
    "svacor"
  ],
  "_datasets": [
    {
      "name": "SE",
      "title": "Example dataset",
      "object": "SE",
      "file": "SE.RData",
      "class": [
        "SummarizedExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "aggSE",
      "title": "aggSE",
      "topics": [
        "aggSE"
      ]
    },
    {
      "page": "castSE",
      "title": "castSE",
      "topics": [
        "castSE"
      ]
    },
    {
      "page": "data",
      "title": "Example dataset",
      "topics": [
        "data",
        "SE"
      ]
    },
    {
      "page": "flattenPB",
      "title": "flattenPB",
      "topics": [
        "flattenPB"
      ]
    },
    {
      "page": "log2FC",
      "title": "log2FC",
      "topics": [
        "log2FC"
      ]
    },
    {
      "page": "mergeSEs",
      "title": "mergeSEs",
      "topics": [
        "mergeSEs"
      ]
    },
    {
      "page": "resetAllSEtoolsOptions",
      "title": "resetAllSEtoolsOptions",
      "topics": [
        "resetAllSEtoolsOptions"
      ]
    },
    {
      "page": "se2xls",
      "title": "se2xlsx",
      "topics": [
        "se2xls"
      ]
    },
    {
      "page": "sehm",
      "title": "sehm",
      "topics": [
        "sehm"
      ]
    },
    {
      "page": "svacor",
      "title": "svacor",
      "topics": [
        "svacor"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/SEtools/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "annotate",
    "AnnotationDbi",
    "askpass",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "ca",
    "cachem",
    "circlize",
    "cli",
    "clue",
    "cluster",
    "codetools",
    "colorspace",
    "ComplexHeatmap",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "DelayedArray",
    "DESeq2",
    "digest",
    "doParallel",
    "edgeR",
    "farver",
    "fastmap",
    "foreach",
    "formatR",
    "futile.logger",
    "futile.options",
    "gclus",
    "genefilter",
    "generics",
    "GenomicRanges",
    "GetoptLong",
    "ggplot2",
    "GlobalOptions",
    "glue",
    "gtable",
    "httr",
    "IRanges",
    "isoband",
    "iterators",
    "jsonlite",
    "KEGGREST",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "locfit",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mgcv",
    "mime",
    "nlme",
    "openssl",
    "openxlsx",
    "permute",
    "pheatmap",
    "pkgconfig",
    "png",
    "qap",
    "R6",
    "randomcoloR",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "registry",
    "rjson",
    "rlang",
    "RSQLite",
    "Rtsne",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "sechm",
    "Seqinfo",
    "seriation",
    "shape",
    "snow",
    "SparseArray",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sva",
    "sys",
    "TSP",
    "V8",
    "vctrs",
    "vegan",
    "viridisLite",
    "withr",
    "XML",
    "xtable",
    "XVector",
    "zip"
  ],
  "_vignettes": [
    {
      "source": "SEtools.Rmd",
      "filename": "SEtools.html",
      "title": "SEtools",
      "author": "Pierre-Luc Germain",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Getting started",
        "Package installation",
        "Example data",
        "Merging and aggregating SEs",
        "Merging by rowData columns",
        "Aggregating a SE",
        "Other convenience functions",
        "Session info"
      ],
      "created": "2019-06-15 16:27:36",
      "modified": "2022-11-27 13:27:17",
      "commits": 20
    }
  ],
  "_score": 6.242044239369551,
  "_indexed": true,
  "_nocasepkg": "setools",
  "_universes": [
    "bioc",
    "plger"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.27.0",
      "date": "2026-05-30T10:32:29.000Z",
      "distro": "noble",
      "commit": "67898208e54f2d58b682dd58d6f64fee3a025670",
      "fileid": "1761e1a1d0ab23a8ca24c0fec3069bbfca9968d4cdf53157cd6955644b2ee833",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677092643"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.27.0",
      "date": "2026-05-30T10:32:50.000Z",
      "distro": "noble",
      "commit": "67898208e54f2d58b682dd58d6f64fee3a025670",
      "fileid": "ef1bb9406f3869cd5420ce86d4c3029a8fc65d6e8fc52049f02e559281240b4f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677092643"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.27.0",
      "date": "2026-05-30T14:54:47.000Z",
      "commit": "67898208e54f2d58b682dd58d6f64fee3a025670",
      "fileid": "c5e58b7365244bbf9f5ab8db5809e35e0a65a58eecc0f690625965ff81f9088b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677092643"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.27.0",
      "date": "2026-05-30T14:55:11.000Z",
      "commit": "67898208e54f2d58b682dd58d6f64fee3a025670",
      "fileid": "cb4173d10bf3d4ea233ca64253d38cc76570723784872e3e7c4a1dae6148ce87",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677092643"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.27.0",
      "date": "2026-05-30T10:31:44.000Z",
      "commit": "67898208e54f2d58b682dd58d6f64fee3a025670",
      "fileid": "8fcdb598ac2e1b42ca7bbddac99cbc517043aaf8d189d6355d324e511f62da9b",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677092643"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.27.0",
      "date": "2026-05-30T10:31:50.000Z",
      "commit": "67898208e54f2d58b682dd58d6f64fee3a025670",
      "fileid": "83be94ab073caeef120155faedb7a233c1ff3f32b123c212f93e215c6facbf0c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677092643"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.27.0",
      "date": "2026-05-30T10:31:21.000Z",
      "commit": "67898208e54f2d58b682dd58d6f64fee3a025670",
      "fileid": "b28bb414fba230124e3a2b301504ba9a401fbef1063145852c4707e60478ebee",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677092643"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.27.0",
      "date": "2026-05-30T10:31:24.000Z",
      "commit": "67898208e54f2d58b682dd58d6f64fee3a025670",
      "fileid": "e133a34e84ae2f40a1c6238cddbba2c599f28b1d79bdb9ed975d7a07422518fa",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677092643"
    }
  ]
}