{
  "_id": "6a1b0bdf1d7bb097a0a076ef",
  "Package": "scTGIF",
  "Type": "Package",
  "Title": "Cell type annotation for unannotated single-cell RNA-Seq data",
  "Version": "1.26.0",
  "Authors@R": "person(\"Koki\", \"Tsuyuzaki\", role = c(\"aut\", \"cre\"),\nemail = \"k.t.the-answer@hotmail.co.jp\")",
  "Description": "scTGIF connects the cells and the related gene functions\nwithout cell type label.",
  "License": "Artistic-2.0",
  "biocViews": "DimensionReduction, QualityControl, SingleCell, Software,\nGeneExpression",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libabsl-dev cmake libfontconfig1-dev\nlibfreetype6-dev libgdal-dev gdal-bin libgeos-dev libglpk-dev\nmake libicu-dev libpng-dev libuv1-dev libxml2-dev libssl-dev\nlibproj-dev libsqlite3-dev libudunits2-dev libnode-dev\nzlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:51:22 UTC",
  "RemoteUrl": "https://github.com/bioc/scTGIF",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "a6e458985ab0f2d0ef63e6960b80d5b46bd619ae",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 11:01:46 UTC",
    "User": "root"
  },
  "Author": "Koki Tsuyuzaki [aut, cre]",
  "Maintainer": "Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>",
  "MD5sum": "f3e57bbc27cc1eb7b30c0326272257ad",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "scTGIF_1.26.0.tar.gz",
  "_fileid": "a22ebaf77bf0a2fdbfd05220d0977cd7b21caef80b7b2a45a6fbbf74cce464ae",
  "_filesize": 2416629,
  "_sha256": "a22ebaf77bf0a2fdbfd05220d0977cd7b21caef80b7b2a45a6fbbf74cce464ae",
  "_created": "2026-05-30T11:01:46.000Z",
  "_published": "2026-05-30T16:10:07.510Z",
  "_jobs": [
    {
      "job": 78644358344,
      "time": 210,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7307780580"
    },
    {
      "job": 78644358357,
      "time": 415,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307798439"
    },
    {
      "job": 78644358350,
      "time": 362,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307793995"
    },
    {
      "job": 78644358353,
      "time": 198,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7309502790"
    },
    {
      "job": 78644358340,
      "time": 297,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7309511031"
    },
    {
      "job": 78643838745,
      "time": 356,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307710012"
    },
    {
      "job": 78644358341,
      "time": 164,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307776390"
    },
    {
      "job": 78644358354,
      "time": 632,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307815991"
    },
    {
      "job": 78644358347,
      "time": 580,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307811697"
    },
    {
      "job": 78644358356,
      "time": 256,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307783549"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 13
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681010951",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/scTGIF",
  "_commit": {
    "id": "a6e458985ab0f2d0ef63e6960b80d5b46bd619ae",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n",
    "time": 1777380682
  },
  "_maintainer": {
    "name": "Koki Tsuyuzaki",
    "email": "k.t.the-answer@hotmail.co.jp",
    "login": "kokitsuyuzaki",
    "description": "",
    "uuid": 2173745
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.6.0",
      "role": "Depends"
    },
    {
      "package": "GSEABase",
      "role": "Imports"
    },
    {
      "package": "Biobase",
      "role": "Imports"
    },
    {
      "package": "SingleCellExperiment",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Imports"
    },
    {
      "package": "plotly",
      "role": "Imports"
    },
    {
      "package": "tagcloud",
      "role": "Imports"
    },
    {
      "package": "rmarkdown",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "nnTensor",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "msigdbr",
      "role": "Imports"
    },
    {
      "package": "schex",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.27.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.26.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "dimensionreduction",
    "qualitycontrol",
    "singlecell",
    "software",
    "geneexpression"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 380,
    "source": "https://www.bioconductor.org/packages/stats/bioc/scTGIF"
  },
  "_searchresults": 6,
  "_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/scTGIF.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "calcTGIF",
    "cellMarkerToGmt",
    "convertRowID",
    "reportTGIF",
    "settingTGIF"
  ],
  "_datasets": [
    {
      "name": "DistalLungEpithelium",
      "title": "Gene expression matrix of DistalLungEpithelium dataset containing five cluster.",
      "object": "DistalLungEpithelium",
      "file": "DistalLungEpithelium.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "1",
        "2",
        "3",
        "4",
        "5",
        "6",
        "7",
        "8",
        "9",
        "10",
        "11",
        "12",
        "13",
        "14",
        "15",
        "16",
        "17",
        "18",
        "19",
        "20",
        "21",
        "22",
        "23",
        "24",
        "25",
        "26",
        "27",
        "28",
        "29",
        "30",
        "31",
        "32",
        "33",
        "34",
        "35",
        "36",
        "37",
        "38",
        "39",
        "40",
        "41",
        "42",
        "43",
        "44",
        "45",
        "46",
        "47",
        "48",
        "49",
        "50",
        "51",
        "52",
        "53",
        "54",
        "55",
        "56",
        "57",
        "58",
        "59",
        "60",
        "61",
        "62",
        "63",
        "64",
        "65",
        "66",
        "67",
        "68",
        "69",
        "70",
        "71",
        "72",
        "73",
        "74",
        "75",
        "76",
        "77",
        "78",
        "79",
        "80"
      ],
      "rows": 3397,
      "table": true,
      "tojson": true
    },
    {
      "name": "label.DistalLungEpithelium",
      "title": "Cellular label of DistalLungEpithelium dataset containing five cluster.",
      "object": "label.DistalLungEpithelium",
      "file": "label.DistalLungEpithelium.rda",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "pca.DistalLungEpithelium",
      "title": "The result of PCA of the DistalLungEpithelium dataset.",
      "object": "pca.DistalLungEpithelium",
      "file": "pca.DistalLungEpithelium.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "PC1",
        "PC2"
      ],
      "rows": 80,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "scTGIF-package",
      "title": "Cell type annotation for unannotated single-cell RNA-Seq data",
      "topics": [
        "scTGIF-package",
        "scTGIF"
      ]
    },
    {
      "page": "calcTGIF",
      "title": "Function for connecting cellular patterns and functional patterns using jNMF",
      "topics": [
        "calcTGIF",
        "calcTGIF,SingleCellExperiment-method"
      ]
    },
    {
      "page": "cellMarkerToGmt",
      "title": "A function to convert the CellMarker data to GMT files.",
      "topics": [
        "cellMarkerToGmt"
      ]
    },
    {
      "page": "convertRowID",
      "title": "A function to change the row names of a matrix.",
      "topics": [
        "convertRowID"
      ]
    },
    {
      "page": "DistalLungEpithelium",
      "title": "Gene expression matrix of DistalLungEpithelium dataset containing five cluster.",
      "topics": [
        "DistalLungEpithelium"
      ]
    },
    {
      "page": "label.DistalLungEpithelium",
      "title": "Cellular label of DistalLungEpithelium dataset containing five cluster.",
      "topics": [
        "label.DistalLungEpithelium"
      ]
    },
    {
      "page": "pca.DistalLungEpithelium",
      "title": "The result of PCA of the DistalLungEpithelium dataset.",
      "topics": [
        "pca.DistalLungEpithelium"
      ]
    },
    {
      "page": "reportTGIF",
      "title": "Function for reporting the result of 'calcTGIF' function",
      "topics": [
        "reportTGIF",
        "reportTGIF,SingleCellExperiment-method"
      ]
    },
    {
      "page": "settingTGIF",
      "title": "Paramter setting for scTGIF",
      "topics": [
        "settingTGIF",
        "settingTGIF,SingleCellExperiment-method"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/scTGIF/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "annotate",
    "AnnotationDbi",
    "askpass",
    "assertthat",
    "babelgene",
    "base64enc",
    "Biobase",
    "BiocGenerics",
    "BiocManager",
    "BiocStyle",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "bookdown",
    "bslib",
    "cachem",
    "class",
    "classInt",
    "cli",
    "cluster",
    "concaveman",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "data.table",
    "DBI",
    "DelayedArray",
    "digest",
    "dotCall64",
    "dplyr",
    "e1071",
    "entropy",
    "evaluate",
    "farver",
    "fastmap",
    "fields",
    "fontawesome",
    "fs",
    "generics",
    "GenomicRanges",
    "ggforce",
    "ggplot2",
    "glue",
    "graph",
    "GSEABase",
    "gtable",
    "hexbin",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httr",
    "igraph",
    "IRanges",
    "isoband",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "KernSmooth",
    "knitr",
    "labeling",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "maps",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "misc3d",
    "msigdbr",
    "nnTensor",
    "openssl",
    "otel",
    "pillar",
    "pkgconfig",
    "plot3D",
    "plotly",
    "png",
    "polyclip",
    "promises",
    "proxy",
    "purrr",
    "R6",
    "RANN",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "rlang",
    "rmarkdown",
    "RSpectra",
    "RSQLite",
    "rTensor",
    "s2",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "schex",
    "Seqinfo",
    "sf",
    "SingleCellExperiment",
    "spam",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "systemfonts",
    "tagcloud",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "tweenr",
    "units",
    "utf8",
    "V8",
    "vctrs",
    "Vicus",
    "viridisLite",
    "withr",
    "wk",
    "xfun",
    "XML",
    "xtable",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "scTGIF.Rmd",
      "filename": "scTGIF.html",
      "title": "Annotation for unannotated single-cell RNA-Seq data by scTGIF",
      "author": "Koki Tsuyuzaki, Itoshi Nikaido",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "About scTGIF",
        "Usage",
        "Test data",
        "Parameter setting : settingTGIF",
        "Calculate attention maps and map-related gene functions: calcTGIF",
        "HTML Report : reportTGIF",
        "Session information"
      ],
      "created": "2019-08-14 04:15:59",
      "modified": "2020-06-27 05:19:44",
      "commits": 5
    }
  ],
  "_score": 4,
  "_indexed": false,
  "_nocasepkg": "sctgif",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://bioc.r-universe.dev/scTGIF",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.26.0",
      "date": "2026-05-30T11:15:46.000Z",
      "distro": "noble",
      "commit": "a6e458985ab0f2d0ef63e6960b80d5b46bd619ae",
      "fileid": "de3f23c0593fa95a78de99aa969715f12306509cda0fad1561e7ed3228fba4b9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681010951"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.26.0",
      "date": "2026-05-30T11:14:54.000Z",
      "distro": "noble",
      "commit": "a6e458985ab0f2d0ef63e6960b80d5b46bd619ae",
      "fileid": "c6a6c1bdd8721e8d2b68acd41439bce67a46bd0bbd32178d023cd4bf9a5f9f45",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681010951"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.26.0",
      "date": "2026-05-30T16:06:26.000Z",
      "commit": "a6e458985ab0f2d0ef63e6960b80d5b46bd619ae",
      "fileid": "4aa7dadbb738f667ef567af3dc001c8cdfebe6ee1d41b2d8caca474d4b19851b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681010951"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.26.0",
      "date": "2026-05-30T16:06:42.000Z",
      "commit": "a6e458985ab0f2d0ef63e6960b80d5b46bd619ae",
      "fileid": "2878d0dee3d74e2726c4c4940647e6111227efd0a3c980282ce419cf6d467ff8",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681010951"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.26.0",
      "date": "2026-05-30T11:14:46.000Z",
      "commit": "a6e458985ab0f2d0ef63e6960b80d5b46bd619ae",
      "fileid": "5858dd46538cbd9c1436417a62aa2b8df45666bbb1ff620103c649812eea10ca",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681010951"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.26.0",
      "date": "2026-05-30T11:18:59.000Z",
      "commit": "a6e458985ab0f2d0ef63e6960b80d5b46bd619ae",
      "fileid": "f60c0c252d6776040f3b0bfca5104ab0b0e3e985dd1fc8885d293ea9713efe36",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681010951"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.26.0",
      "date": "2026-05-30T11:18:11.000Z",
      "commit": "a6e458985ab0f2d0ef63e6960b80d5b46bd619ae",
      "fileid": "afd0df4224bf449b78fe87e334f2ad5493854b599ff1a2db514e5818063c9f83",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681010951"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.26.0",
      "date": "2026-05-30T11:12:57.000Z",
      "commit": "a6e458985ab0f2d0ef63e6960b80d5b46bd619ae",
      "fileid": "af312879aeb3f2c211defe22fa711a77d45002a42fe5c318dbd5a1da79737e78",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681010951"
    }
  ]
}