{
  "_id": "6a1be6071d7bb097a0a1a3cd",
  "Package": "NetActivity",
  "Type": "Package",
  "Title": "Compute gene set scores from a deep learning framework",
  "Version": "1.15.0",
  "Authors@R": "c(person(\"Carlos\", \"Ruiz-Arenas\", , \"carlos.ruiza@upf.edu\", role = c(\"aut\", \"cre\")))",
  "Description": "#' NetActivity enables to compute gene set scores from\npreviously trained sparsely-connected autoencoders. The package\ncontains a function to prepare the data\n(`prepareSummarizedExperiment`) and a function to compute the\ngene set scores (`computeGeneSetScores`). The package\n`NetActivityData` contains different pre-trained models to be\ndirectly applied to the data. Alternatively, the users might\nuse the package to compute gene set scores using custom models.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Config/testthat/edition": "3",
  "biocViews": "RNASeq, Microarray, Transcription, FunctionalGenomics, GO,\nGeneExpression, Pathways, Software",
  "RoxygenNote": "7.2.1",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:59:23 UTC",
  "RemoteUrl": "https://github.com/bioc/NetActivity",
  "RemoteRef": "HEAD",
  "RemoteSha": "0e261497beadffad703b9eddaabca33b2a0460a4",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-31 06:38:49 UTC",
    "User": "root"
  },
  "Author": "Carlos Ruiz-Arenas [aut, cre]",
  "Maintainer": "Carlos Ruiz-Arenas <carlos.ruiza@upf.edu>",
  "MD5sum": "43e2fe2a814fb792161a6c80f5631137",
  "_user": "bioc",
  "_type": "src",
  "_file": "NetActivity_1.15.0.tar.gz",
  "_fileid": "e2591fb5c6b20d0a7133390acec5358bb9b178ff80608234a0ac5a7f9eeac85b",
  "_filesize": 232527,
  "_sha256": "e2591fb5c6b20d0a7133390acec5358bb9b178ff80608234a0ac5a7f9eeac85b",
  "_created": "2026-05-31T06:38:49.000Z",
  "_published": "2026-05-31T07:40:55.576Z",
  "_jobs": [
    {
      "job": 78706143709,
      "time": 246,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7314521336"
    },
    {
      "job": 78706143716,
      "time": 370,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7314533709"
    },
    {
      "job": 78706143715,
      "time": 380,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7314534720"
    },
    {
      "job": 78706143704,
      "time": 306,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7314903538"
    },
    {
      "job": 78706143708,
      "time": 279,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7314899904"
    },
    {
      "job": 78705839623,
      "time": 329,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7314495682"
    },
    {
      "job": 78706143706,
      "time": 203,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7314517274"
    },
    {
      "job": 78706143725,
      "time": 305,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7314527052"
    },
    {
      "job": 78706143744,
      "time": 317,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7314528200"
    },
    {
      "job": 78706143717,
      "time": 314,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7314527999"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 7
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26705473414",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/NetActivity",
  "_commit": {
    "id": "0e261497beadffad703b9eddaabca33b2a0460a4",
    "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": 1777381163
  },
  "_maintainer": {
    "name": "Carlos Ruiz-Arenas",
    "email": "carlos.ruiza@upf.edu"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "airway",
      "role": "Imports"
    },
    {
      "package": "DelayedArray",
      "role": "Imports"
    },
    {
      "package": "DelayedMatrixStats",
      "role": "Imports"
    },
    {
      "package": "DESeq2",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "NetActivityData",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "AnnotationDbi",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "Fletcher2013a",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "tidyverse",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.15.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.14.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "rnaseq",
    "microarray",
    "transcription",
    "functionalgenomics",
    "go",
    "geneexpression",
    "pathways",
    "software"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 276,
    "source": "https://www.bioconductor.org/packages/stats/bioc/NetActivity"
  },
  "_searchresults": 29,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NetActivity.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "computeGeneSetScores",
    "prepareSummarizedExperiment"
  ],
  "_help": [
    {
      "page": "computeGeneSetScores",
      "title": "Compute gene set scores",
      "topics": [
        "computeGeneSetScores"
      ]
    },
    {
      "page": "NetActivity",
      "title": "NetActivity: compute gene set scores from a deep learning framework",
      "topics": [
        "NetActivity"
      ]
    },
    {
      "page": "prepareSummarizedExperiment",
      "title": "Prepare a SummarizedExperiment for computing gene set scores computation",
      "topics": [
        "prepareSummarizedExperiment"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/NetActivity/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "airway",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "cli",
    "codetools",
    "cpp11",
    "DelayedArray",
    "DelayedMatrixStats",
    "DESeq2",
    "farver",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "IRanges",
    "isoband",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "locfit",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "NetActivityData",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "rlang",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "sparseMatrixStats",
    "SummarizedExperiment",
    "vctrs",
    "viridisLite",
    "withr",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "NetActivity.Rmd",
      "filename": "NetActivity.html",
      "title": "Gene set scores computation with NetActivity",
      "author": "Carlos Ruiz Arenas",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation",
        "Introduction",
        "Pre-processing",
        "RNAseq",
        "Microarray data",
        "Computing the scores",
        "Differential gene set scores analysis"
      ],
      "created": "2022-09-13 08:22:20",
      "modified": "2022-10-17 14:02:17",
      "commits": 5
    }
  ],
  "_score": 4.4623979978989565,
  "_indexed": true,
  "_nocasepkg": "netactivity",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.15.0",
      "date": "2026-05-31T06:42:55.000Z",
      "distro": "noble",
      "commit": "0e261497beadffad703b9eddaabca33b2a0460a4",
      "fileid": "b4008eb3b509a40f040fea1c82f3569a6cba5c1ff3858b12d939667f9c1bd1b0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705473414"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.15.0",
      "date": "2026-05-31T06:43:02.000Z",
      "distro": "noble",
      "commit": "0e261497beadffad703b9eddaabca33b2a0460a4",
      "fileid": "70b239ea0c0175fecf33497e9bb788d8fe9b9acc1104fa00b3ddd4d71c4ba877",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705473414"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.15.0",
      "date": "2026-05-31T07:38:05.000Z",
      "commit": "0e261497beadffad703b9eddaabca33b2a0460a4",
      "fileid": "71887f304b4ef72e60bda4ce55d4214fad0fc00fff4f03627fe55e9dd11456d5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705473414"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.15.0",
      "date": "2026-05-31T07:37:24.000Z",
      "commit": "0e261497beadffad703b9eddaabca33b2a0460a4",
      "fileid": "9faab0183c86fbaf42a1fc10bee71c4b1203fdb1c90bcd3c79490088f669dd8a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705473414"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.15.0",
      "date": "2026-05-31T06:42:42.000Z",
      "commit": "0e261497beadffad703b9eddaabca33b2a0460a4",
      "fileid": "070dc9ff49aeca5138feea8dff1ba116653f80fb2755b7bc54e076a547a1a0e9",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705473414"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.15.0",
      "date": "2026-05-31T06:41:42.000Z",
      "commit": "0e261497beadffad703b9eddaabca33b2a0460a4",
      "fileid": "55a709edccbbaed72a9a8782a476fe2a97c644ee46378cd5f06ab939d2533768",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705473414"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.15.0",
      "date": "2026-05-31T06:41:50.000Z",
      "commit": "0e261497beadffad703b9eddaabca33b2a0460a4",
      "fileid": "3a41a227d0fc073c2b24e51e8f00e31e178995edf6d23958a84cbf17d819459f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705473414"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.15.0",
      "date": "2026-05-31T06:41:36.000Z",
      "commit": "0e261497beadffad703b9eddaabca33b2a0460a4",
      "fileid": "40c79638590e0356194852553d01878139a8b3aad8e24942a0a00e33ad610a5e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705473414"
    }
  ]
}