{
  "_id": "6a1ac1551d7bb097a09d8102",
  "Package": "NanoTube",
  "Type": "Package",
  "Title": "An Easy Pipeline for NanoString nCounter Data Analysis",
  "Version": "1.19.0",
  "Date": "2023-05-31",
  "Authors@R": "c(person(\"Caleb\", \"Class\", email=\"cclass@butler.edu\",\nrole = c(\"cre\", \"aut\"),\ncomment = c(ORCID = \"0000-0003-3130-3613\")),\nperson(\"Caiden\", \"Lukan\", role = \"ctb\"))",
  "VignetteBuilder": "knitr",
  "Description": "NanoTube includes functions for the processing, quality\ncontrol, analysis, and visualization of NanoString nCounter\ndata. Analysis functions include differential analysis and gene\nset analysis methods, as well as postprocessing steps to help\nunderstand the results. Additional functions are included to\nenable interoperability with other Bioconductor NanoString data\nanalysis packages.",
  "License": "GPL-3 + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "false",
  "RoxygenNote": "7.2.1",
  "biocViews": "Software, GeneExpression, DifferentialExpression,\nQualityControl",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:56:22 UTC",
  "RemoteUrl": "https://github.com/bioc/NanoTube",
  "RemoteRef": "HEAD",
  "RemoteSha": "cf02f2e565efab61e4cd8a7c9581da105669f795",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 07:26:29 UTC",
    "User": "root"
  },
  "Author": "Caleb Class [cre, aut] (ORCID: <https://orcid.org/0000-0003-3130-3613>),\nCaiden Lukan [ctb]",
  "Maintainer": "Caleb Class <cclass@butler.edu>",
  "MD5sum": "791098d3834199bd05a7cca89de1fe2d",
  "_user": "bioc",
  "_type": "src",
  "_file": "NanoTube_1.19.0.tar.gz",
  "_fileid": "6908df89671bedd5f605099d4f8162441a45a29143b67e320bb604dba8430aeb",
  "_filesize": 1671321,
  "_sha256": "6908df89671bedd5f605099d4f8162441a45a29143b67e320bb604dba8430aeb",
  "_created": "2026-05-30T07:26:29.000Z",
  "_published": "2026-05-30T10:52:05.601Z",
  "_jobs": [
    {
      "job": 78633421501,
      "time": 336,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306495036"
    },
    {
      "job": 78633421511,
      "time": 288,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306490068"
    },
    {
      "job": 78633421509,
      "time": 354,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306496775"
    },
    {
      "job": 78633421508,
      "time": 157,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307589113"
    },
    {
      "job": 78633421513,
      "time": 178,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307593646"
    },
    {
      "job": 78633159586,
      "time": 290,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306456846"
    },
    {
      "job": 78633421504,
      "time": 182,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306478548"
    },
    {
      "job": 78633421518,
      "time": 257,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306486757"
    },
    {
      "job": 78633421525,
      "time": 226,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7306483446"
    },
    {
      "job": 78633421510,
      "time": 230,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306483955"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 11
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677942302",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/NanoTube",
  "_commit": {
    "id": "cf02f2e565efab61e4cd8a7c9581da105669f795",
    "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": 1777380982
  },
  "_maintainer": {
    "name": "Caleb Class",
    "email": "cclass@butler.edu",
    "orcid": "0000-0003-3130-3613"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "role": "Depends"
    },
    {
      "package": "ggplot2",
      "role": "Depends"
    },
    {
      "package": "limma",
      "role": "Depends"
    },
    {
      "package": "fgsea",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "reshape",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Suggests"
    },
    {
      "package": "kableExtra",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "NanoStringDiff",
      "role": "Suggests"
    },
    {
      "package": "pheatmap",
      "role": "Suggests"
    },
    {
      "package": "plotly",
      "role": "Suggests"
    },
    {
      "package": "rlang",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "ruv",
      "role": "Suggests"
    },
    {
      "package": "RUVSeq",
      "role": "Suggests"
    },
    {
      "package": "shiny",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "xlsx",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.19.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.18.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "geneexpression",
    "differentialexpression",
    "qualitycontrol"
  ],
  "_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/NanoTube"
  },
  "_searchresults": 8,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NanoTube.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "deVolcano",
    "fgseaPostprocessing",
    "fgseaPostprocessingXLSX",
    "fgseaToLEdge",
    "gm_mean",
    "groupedGSEAtoStackedReport",
    "groupFGSEA",
    "limmaToFGSEA",
    "makeDiffExprFile",
    "makeNanoStringSetFromEset",
    "nanostringPCA",
    "negativeQC",
    "normalize_housekeeping",
    "normalize_pos_controls",
    "nsdiffToFGSEA",
    "positiveQC",
    "processNanostringData",
    "read_cpdb_sourceDBs",
    "read_cpdb_tab",
    "read_merge_rcc",
    "read_rcc",
    "read_sampleData",
    "remove_background",
    "runLimmaAnalysis",
    "untar_dirs",
    "unzip_dirs"
  ],
  "_datasets": [
    {
      "name": "ExamplePathways",
      "title": "Example pathway database",
      "object": "ExamplePathways",
      "file": "ExamplePathways.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "ExampleResults",
      "title": "Example results from runLimmaAnalysis",
      "object": "ExampleResults",
      "file": "ExampleResults.rda",
      "class": [
        "MArrayLM"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "deVolcano",
      "title": "Draw volcano plot of differential expression results",
      "topics": [
        "deVolcano"
      ]
    },
    {
      "page": "ExamplePathways",
      "title": "Example pathway database",
      "topics": [
        "ExamplePathways"
      ]
    },
    {
      "page": "ExampleResults",
      "title": "Example results from runLimmaAnalysis",
      "topics": [
        "ExampleResults"
      ]
    },
    {
      "page": "fgseaPostprocessing",
      "title": "Postprocessing for GSEA analyses",
      "topics": [
        "fgseaPostprocessing"
      ]
    },
    {
      "page": "fgseaPostprocessingXLSX",
      "title": "Postprocessing for GSEA analyses for Excel",
      "topics": [
        "fgseaPostprocessingXLSX"
      ]
    },
    {
      "page": "fgseaToLEdge",
      "title": "Generate leading edge matrix from fgsea results.",
      "topics": [
        "fgseaToLEdge"
      ]
    },
    {
      "page": "gm_mean",
      "title": "Calculate the geometric mean",
      "topics": [
        "gm_mean"
      ]
    },
    {
      "page": "groupedGSEAtoStackedReport",
      "title": "Build a report from gene set enrichment results.",
      "topics": [
        "groupedGSEAtoStackedReport"
      ]
    },
    {
      "page": "groupFGSEA",
      "title": "Cluster gene set analysis results",
      "topics": [
        "groupFGSEA"
      ]
    },
    {
      "page": "limmaToFGSEA",
      "title": "Run gene set enrichment analysis using DE results.",
      "topics": [
        "limmaToFGSEA"
      ]
    },
    {
      "page": "makeDiffExprFile",
      "title": "Make differential expression results file.",
      "topics": [
        "makeDiffExprFile"
      ]
    },
    {
      "page": "makeFGSEAmasterTable",
      "title": "Make master table of all GSEA results",
      "topics": [
        "makeFGSEAmasterTable"
      ]
    },
    {
      "page": "makeNanoStringSetFromEset",
      "title": "Convert NanoString ExpressionSet to NanoStringSet",
      "topics": [
        "makeNanoStringSetFromEset"
      ]
    },
    {
      "page": "nanostringPCA",
      "title": "Plot PCA",
      "topics": [
        "nanostringPCA"
      ]
    },
    {
      "page": "NanoTube",
      "title": "NanoTube",
      "topics": [
        "NanoTube"
      ]
    },
    {
      "page": "negativeQC",
      "title": "Calculate negative control statistics",
      "topics": [
        "negativeQC"
      ]
    },
    {
      "page": "normalize_housekeeping",
      "title": "Housekeeping gene normalization",
      "topics": [
        "normalize_housekeeping"
      ]
    },
    {
      "page": "normalize_pos_controls",
      "title": "Positive control gene normalization",
      "topics": [
        "normalize_pos_controls"
      ]
    },
    {
      "page": "nsdiffToFGSEA",
      "title": "Run gene set enrichment analysis using DE results.",
      "topics": [
        "nsdiffToFGSEA"
      ]
    },
    {
      "page": "positiveQC",
      "title": "Calculate positive control statistics",
      "topics": [
        "positiveQC"
      ]
    },
    {
      "page": "processNanostringData",
      "title": "Process NanoString nCounter gene expression data.",
      "topics": [
        "processNanostringData"
      ]
    },
    {
      "page": "read_cpdb_sourceDBs",
      "title": "Identify source databases from a .tab file",
      "topics": [
        "read_cpdb_sourceDBs"
      ]
    },
    {
      "page": "read_cpdb_tab",
      "title": "Read .tab file.",
      "topics": [
        "read_cpdb_tab"
      ]
    },
    {
      "page": "read_merge_rcc",
      "title": "Merge multiple .rcc files",
      "topics": [
        "read_merge_rcc"
      ]
    },
    {
      "page": "read_rcc",
      "title": "Read .rcc file",
      "topics": [
        "read_rcc"
      ]
    },
    {
      "page": "read_sampleData",
      "title": "Read in a sample data table.",
      "topics": [
        "read_sampleData"
      ]
    },
    {
      "page": "remove_background",
      "title": "Assess background expression",
      "topics": [
        "remove_background"
      ]
    },
    {
      "page": "runLimmaAnalysis",
      "title": "Conduct differential expression analysis",
      "topics": [
        "runLimmaAnalysis"
      ]
    },
    {
      "page": "untar_dirs",
      "title": "Untar",
      "topics": [
        "untar_dirs"
      ]
    },
    {
      "page": "unzip_dirs",
      "title": "Unzip",
      "topics": [
        "unzip_dirs"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/NanoTube/raw/HEAD/README.md",
  "_rundeps": [
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "cli",
    "codetools",
    "cowplot",
    "cpp11",
    "data.table",
    "farver",
    "fastmatch",
    "fgsea",
    "formatR",
    "futile.logger",
    "futile.options",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "Matrix",
    "plyr",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "reshape",
    "rlang",
    "S7",
    "scales",
    "snow",
    "statmod",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "NanoTube.Rmd",
      "filename": "NanoTube.html",
      "title": "Analyzing NanoString nCounter Data with the NanoTube",
      "author": "Caleb A Class",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Abstract",
        "A basic workflow",
        "Processing Data",
        "From RCC files",
        "From Other files",
        "Normalization",
        "nSolver Normalization",
        "RUV-III Normalization",
        "RUVg Normalization",
        "Assessing Normalization Performance",
        "RLE Plots",
        "Principal components analysis",
        "Quality Control",
        "Data Analysis",
        "Differential expression analysis",
        "Using Limma",
        "Using NanoStringDiff",
        "Gene set analysis",
        "Exporting GSEA results",
        "References"
      ],
      "created": "2020-09-29 19:25:14",
      "modified": "2023-03-08 17:59:38",
      "commits": 17
    }
  ],
  "_score": 4,
  "_indexed": true,
  "_nocasepkg": "nanotube",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.19.0",
      "date": "2026-05-30T07:30:26.000Z",
      "distro": "noble",
      "commit": "cf02f2e565efab61e4cd8a7c9581da105669f795",
      "fileid": "ba3d81d98ca337325a5e54bd8be4fd8454bfe6684fd791ed0594a96eb2941bb3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677942302"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.19.0",
      "date": "2026-05-30T07:31:30.000Z",
      "distro": "noble",
      "commit": "cf02f2e565efab61e4cd8a7c9581da105669f795",
      "fileid": "40a1f2b9477198b41764a9955bb52a287f2cb81945808635d415b687cc164e44",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677942302"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.19.0",
      "date": "2026-05-30T10:40:41.000Z",
      "commit": "cf02f2e565efab61e4cd8a7c9581da105669f795",
      "fileid": "d83b127294a4ced1f8a5cad2a9fcda5273e2bb8c6c0d96ca257d5e2e936847be",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677942302"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.19.0",
      "date": "2026-05-30T10:41:20.000Z",
      "commit": "cf02f2e565efab61e4cd8a7c9581da105669f795",
      "fileid": "44ddccb3b07c1e8fc8bba326efe8fd91752bed20f0287e44b130cd180ff1cdb7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677942302"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.19.0",
      "date": "2026-05-30T07:29:51.000Z",
      "commit": "cf02f2e565efab61e4cd8a7c9581da105669f795",
      "fileid": "923207c4bdde2bcb0bca2405b1454920d90629c98688f62b2e5b01b31a23e9d2",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677942302"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.19.0",
      "date": "2026-05-30T07:28:53.000Z",
      "commit": "cf02f2e565efab61e4cd8a7c9581da105669f795",
      "fileid": "5fee0ac5603e358828051d4a404d1c59bca540cc92c9e619635709f5f44e2419",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677942302"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.19.0",
      "date": "2026-05-30T07:28:35.000Z",
      "commit": "cf02f2e565efab61e4cd8a7c9581da105669f795",
      "fileid": "ecac4128fd53e0860db74fed79ddd175345a213506075d019a72ccea9b99b44c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677942302"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.19.0",
      "date": "2026-05-30T07:28:26.000Z",
      "commit": "cf02f2e565efab61e4cd8a7c9581da105669f795",
      "fileid": "cb0367b252f2b3f068341a4cc8791b16db5285fb80bc45107c93d9c1b6fa1246",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677942302"
    }
  ]
}