{
  "_id": "6a30fa573efcd9bda434dcbf",
  "Package": "granulator",
  "Type": "Package",
  "Title": "Rapid benchmarking of methods for *in silico* deconvolution of\nbulk RNA-seq data",
  "Version": "1.20.0",
  "Authors@R": "c(person(given = \"Sabina\",\nfamily = \"Pfister\",\nrole = c(\"aut\", \"cre\"),\nemail = \"sabina.pfister@novartis.com\"),\nperson(given = \"Vincent\",\nfamily = \"Kuettel\",\nrole = \"aut\"),\nperson(given = \"Enrico\",\nfamily = \"Ferrero\",\nrole = \"aut\"))",
  "Description": "granulator is an R package for the cell type deconvolution\nof heterogeneous tissues based on bulk RNA-seq data or single\ncell RNA-seq expression profiles. The package provides a\nunified testing interface to rapidly run and benchmark multiple\nstate-of-the-art deconvolution methods. Data for the\ndeconvolution of peripheral blood mononuclear cells (PBMCs)\ninto individual immune cell types is provided as well.",
  "URL": "https://github.com/xanibas/granulator",
  "BugReports": "https://github.com/xanibas/granulator/issues",
  "VignetteBuilder": "knitr",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "FALSE",
  "RoxygenNote": "7.1.1",
  "biocViews": "RNASeq, GeneExpression, DifferentialExpression,\nTranscriptomics, SingleCell, StatisticalMethod, Regression",
  "PackageStatus": "Deprecated",
  "Config/pak/sysreqs": "libabsl-dev libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev libgdal-dev gdal-bin\nlibgeos-dev make libharfbuzz-dev libicu-dev libjpeg-dev\nlibpng-dev libtiff-dev libuv1-dev libwebp-dev libxml2-dev\nlibssl-dev libproj-dev libsqlite3-dev libudunits2-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:55:48 UTC",
  "RemoteUrl": "https://github.com/bioc/granulator",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "b87f30eb2fa20b33d4040542c2d93c1243eae1ff",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-16 07:15:03 UTC",
    "User": "root"
  },
  "Author": "Sabina Pfister [aut, cre],\nVincent Kuettel [aut],\nEnrico Ferrero [aut]",
  "Maintainer": "Sabina Pfister <sabina.pfister@novartis.com>",
  "MD5sum": "f850487eea998a2c15f83513c158990f",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "granulator_1.20.0.tar.gz",
  "_fileid": "c845f6e4a762e67e677e1bce5a1e060eeefddf209acba772e57ecc12a4a55ae1",
  "_filesize": 1249879,
  "_sha256": "c845f6e4a762e67e677e1bce5a1e060eeefddf209acba772e57ecc12a4a55ae1",
  "_created": "2026-06-16T07:15:03.000Z",
  "_published": "2026-06-16T07:25:11.478Z",
  "_jobs": [
    {
      "job": 81601406754,
      "time": 189,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7659887691"
    },
    {
      "job": 81601406751,
      "time": 457,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7659970144"
    },
    {
      "job": 81601406740,
      "time": 465,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7659972600"
    },
    {
      "job": 81601406752,
      "time": 262,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7659921583"
    },
    {
      "job": 81601406744,
      "time": 351,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7659941757"
    },
    {
      "job": 81600347364,
      "time": 391,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7659825327"
    },
    {
      "job": 81601406735,
      "time": 157,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7659874651"
    },
    {
      "job": 81601406746,
      "time": 368,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7659942685"
    },
    {
      "job": 81601406766,
      "time": 354,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7659938083"
    },
    {
      "job": 81601406758,
      "time": 318,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7659926688"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 3,
    "note": 8
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27600563281",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/granulator",
  "_commit": {
    "id": "b87f30eb2fa20b33d4040542c2d93c1243eae1ff",
    "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": 1777380948
  },
  "_maintainer": {
    "name": "Sabina Pfister",
    "email": "sabina.pfister@novartis.com",
    "login": "xanibas",
    "description": "",
    "uuid": 2014543
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1",
      "role": "Depends"
    },
    {
      "package": "cowplot",
      "role": "Imports"
    },
    {
      "package": "e1071",
      "role": "Imports"
    },
    {
      "package": "epiR",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "dtangle",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ggplotify",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "limSolve",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "nnls",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "pheatmap",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-11",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_topics": [
    "rnaseq",
    "geneexpression",
    "differentialexpression",
    "transcriptomics",
    "singlecell",
    "statisticalmethod",
    "regression"
  ],
  "_stars": 3,
  "_contributors": [
    {
      "user": "xanibas",
      "count": 14,
      "uuid": 2014543
    },
    {
      "user": "nturaga",
      "count": 2,
      "uuid": 2746443
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 440,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_devurl": "https://github.com/xanibas/granulator",
  "_searchresults": 17,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/granulator.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "benchmark",
    "correlate",
    "deconvolute",
    "get_decon_methods",
    "get_TPM",
    "load_ABIS",
    "plot_benchmark",
    "plot_correlate",
    "plot_deconvolute",
    "plot_proportions",
    "plot_regress",
    "plot_similarity"
  ],
  "_datasets": [
    {
      "name": "bulkRNAseq_ABIS",
      "title": "PBMCs expression profiles (ABIS dataset)",
      "object": "bulkRNAseq_ABIS",
      "file": "bulkRNAseq_ABIS.RData",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "CYFZ",
        "FY2H",
        "FLWA",
        "453W",
        "684C",
        "CZJE",
        "925L",
        "9JD4",
        "G4YW",
        "4DUY",
        "36TS",
        "CR3L"
      ],
      "rows": 1296,
      "table": true,
      "tojson": true
    },
    {
      "name": "groundTruth_ABIS",
      "title": "PBMCS true cell type proprotions (ABIS dataset)",
      "object": "groundTruth_ABIS",
      "file": "groundTruth_ABIS.RData",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "Monocytes.C",
        "NK",
        "T.CD8.Memory",
        "T.CD4.Naive",
        "T.CD8.Naive",
        "B.Naive",
        "T.CD4.Memory",
        "MAIT",
        "T.gd.Vd2",
        "Neutrophils.LD",
        "T.gd.non.Vd2",
        "Basophils.LD",
        "Monocytes.NC.I",
        "B.Memory",
        "mDCs",
        "pDCs",
        "Plasmablasts",
        "B.Cells",
        "Monocytes",
        "Dendritic.Cells",
        "T.gd",
        "T.Naive",
        "T.Memory",
        "T.Cells"
      ],
      "rows": 12,
      "table": true,
      "tojson": true
    },
    {
      "name": "sigMatrix_ABIS_S0",
      "title": "Signature matrix for deconvolution of PBMCs in 17 cell types",
      "object": "sigMatrix_ABIS_S0",
      "file": "sigMatrix_ABIS_S0.RData",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "Monocytes.C",
        "NK",
        "T.CD8.Memory",
        "T.CD4.Naive",
        "T.CD8.Naive",
        "B.Naive",
        "T.CD4.Memory",
        "MAIT",
        "T.gd.Vd2",
        "Neutrophils.LD",
        "T.gd.non.Vd2",
        "Basophils.LD",
        "Monocytes.NC.I",
        "B.Memory",
        "mDCs",
        "pDCs",
        "Plasmablasts"
      ],
      "rows": 1296,
      "table": true,
      "tojson": true
    },
    {
      "name": "sigMatrix_ABIS_S1",
      "title": "Signature matrix for deconvolution of PBMCs in 13 cell types",
      "object": "sigMatrix_ABIS_S1",
      "file": "sigMatrix_ABIS_S1.RData",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "B.Cells",
        "Basophils.LD",
        "MAIT",
        "mDCs",
        "Monocytes",
        "Neutrophils.LD",
        "NK",
        "pDCs",
        "Plasmablasts",
        "T.CD4.Memory",
        "T.CD8.Memory",
        "T.Naive",
        "T.gd"
      ],
      "rows": 1296,
      "table": true,
      "tojson": true
    },
    {
      "name": "sigMatrix_ABIS_S2",
      "title": "Signature matrix for deconvolution of PBMCs in 11 cell types",
      "object": "sigMatrix_ABIS_S2",
      "file": "sigMatrix_ABIS_S2.RData",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "B.Cells",
        "Basophils.LD",
        "MAIT",
        "Dendritic.Cells",
        "Neutrophils.LD",
        "NK",
        "pDCs",
        "Plasmablasts",
        "T.Memory",
        "T.Naive",
        "T.gd"
      ],
      "rows": 1296,
      "table": true,
      "tojson": true
    },
    {
      "name": "sigMatrix_ABIS_S3",
      "title": "Signature matrix for deconvolution of PBMCs in 9 cell types",
      "object": "sigMatrix_ABIS_S3",
      "file": "sigMatrix_ABIS_S3.RData",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "B.Cells",
        "Basophils.LD",
        "MAIT",
        "Dendritic.Cells",
        "Neutrophils.LD",
        "NK",
        "pDCs",
        "Plasmablasts",
        "T.Cells"
      ],
      "rows": 1296,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "benchmark",
      "title": "Regress estimated cell type proportions against the ground truth",
      "topics": [
        "benchmark"
      ]
    },
    {
      "page": "bulkRNAseq_ABIS",
      "title": "PBMCs expression profiles (ABIS dataset)",
      "topics": [
        "bulkRNAseq_ABIS"
      ]
    },
    {
      "page": "correlate",
      "title": "Pearson correlation of cell type proportions across cell types and methods",
      "topics": [
        "correlate"
      ]
    },
    {
      "page": "deconvolute",
      "title": "Deconvolution from bulk RNAseq",
      "topics": [
        "deconvolute"
      ]
    },
    {
      "page": "get_decon_methods",
      "title": "Deconvolution methods acronyms",
      "topics": [
        "get_decon_methods"
      ]
    },
    {
      "page": "get_TPM",
      "title": "Convert raw counts to TPM",
      "topics": [
        "get_TPM"
      ]
    },
    {
      "page": "groundTruth_ABIS",
      "title": "PBMCS true cell type proprotions (ABIS dataset)",
      "topics": [
        "groundTruth_ABIS"
      ]
    },
    {
      "page": "load_ABIS",
      "title": "Load demo PBMCs deconvolution data",
      "topics": [
        "load_ABIS"
      ]
    },
    {
      "page": "plot_benchmark",
      "title": "Plot benchmarking analysis scores",
      "topics": [
        "plot_benchmark"
      ]
    },
    {
      "page": "plot_correlate",
      "title": "Plot of correlations between deconvolution methods",
      "topics": [
        "plot_correlate"
      ]
    },
    {
      "page": "plot_deconvolute",
      "title": "Estimated cell types across methods",
      "topics": [
        "plot_deconvolute"
      ]
    },
    {
      "page": "plot_proportions",
      "title": "Plot estimated cell type proportions",
      "topics": [
        "plot_proportions"
      ]
    },
    {
      "page": "plot_regress",
      "title": "Plot estimated cell type coefficients against the ground truth",
      "topics": [
        "plot_regress"
      ]
    },
    {
      "page": "plot_similarity",
      "title": "Plot reference profile similariy matrix",
      "topics": [
        "plot_similarity"
      ]
    },
    {
      "page": "sigMatrix_ABIS_S0",
      "title": "Signature matrix for deconvolution of PBMCs in 17 cell types",
      "topics": [
        "sigMatrix_ABIS_S0"
      ]
    },
    {
      "page": "sigMatrix_ABIS_S1",
      "title": "Signature matrix for deconvolution of PBMCs in 13 cell types",
      "topics": [
        "sigMatrix_ABIS_S1"
      ]
    },
    {
      "page": "sigMatrix_ABIS_S2",
      "title": "Signature matrix for deconvolution of PBMCs in 11 cell types",
      "topics": [
        "sigMatrix_ABIS_S2"
      ]
    },
    {
      "page": "sigMatrix_ABIS_S3",
      "title": "Signature matrix for deconvolution of PBMCs in 9 cell types",
      "topics": [
        "sigMatrix_ABIS_S3"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/granulator/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "askpass",
    "base64enc",
    "BiasedUrn",
    "bslib",
    "cachem",
    "class",
    "classInt",
    "cli",
    "cowplot",
    "cpp11",
    "data.table",
    "DBI",
    "DEoptimR",
    "digest",
    "dplyr",
    "dtangle",
    "e1071",
    "epiR",
    "evaluate",
    "farver",
    "fastmap",
    "flextable",
    "fontawesome",
    "fontBitstreamVera",
    "fontLiberation",
    "fontquiver",
    "fs",
    "gdtools",
    "generics",
    "ggplot2",
    "ggplotify",
    "glue",
    "gridGraphics",
    "gtable",
    "highr",
    "htmltools",
    "isoband",
    "jquerylib",
    "jsonlite",
    "KernSmooth",
    "knitr",
    "labeling",
    "lattice",
    "lifecycle",
    "limSolve",
    "lpSolve",
    "lubridate",
    "magrittr",
    "MASS",
    "Matrix",
    "memoise",
    "mime",
    "nnls",
    "officer",
    "openssl",
    "pander",
    "pheatmap",
    "pillar",
    "pkgconfig",
    "proxy",
    "purrr",
    "quadprog",
    "R6",
    "ragg",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "rlang",
    "rmarkdown",
    "s2",
    "S7",
    "sass",
    "scales",
    "sf",
    "stringi",
    "stringr",
    "survival",
    "sys",
    "systemfonts",
    "textshaping",
    "tibble",
    "tidyr",
    "tidyselect",
    "timechange",
    "tinytex",
    "units",
    "utf8",
    "uuid",
    "vctrs",
    "viridisLite",
    "withr",
    "wk",
    "xfun",
    "xml2",
    "yaml",
    "yulab.utils",
    "zip",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "granulator.Rmd",
      "filename": "granulator.html",
      "title": "Deconvolution of bulk RNA-seq data with granulator",
      "author": "Vincent Kuettel, Sabina Pfister, Enrico Ferrero",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Installation",
        "Data",
        "Bulk PBMCs RNA-seq",
        "Reference profiles",
        "Measured cell type proportions",
        "Workflow",
        "Comparing multiple reference profiles",
        "Deconvolution of bulk RNA-seq data",
        "Benchmarking of deconvolution methods",
        "Correlation analysis of deconvoluted proportions",
        "Session Info",
        "References"
      ],
      "created": "2021-05-03 22:40:45",
      "modified": "2021-05-17 06:20:32",
      "commits": 5
    }
  ],
  "_score": 3.8836614351536176,
  "_indexed": false,
  "_nocasepkg": "granulator",
  "_universes": [
    "bioc-release"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.20.0",
      "date": "2026-06-16T07:20:04.000Z",
      "distro": "noble",
      "commit": "b87f30eb2fa20b33d4040542c2d93c1243eae1ff",
      "fileid": "9543e1661ae63f96d2500c07b1e6fec8fb771bcf371db03f7e7bfdf54dac0bec",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27600563281"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.20.0",
      "date": "2026-06-16T07:20:16.000Z",
      "distro": "noble",
      "commit": "b87f30eb2fa20b33d4040542c2d93c1243eae1ff",
      "fileid": "bdad58b08969eec1b14ef34ab810257307e1347fd8cf07f8504ce386ca08735c",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27600563281"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.20.0",
      "date": "2026-06-16T07:18:54.000Z",
      "commit": "b87f30eb2fa20b33d4040542c2d93c1243eae1ff",
      "fileid": "9374636d1c70e712c7820b5877ee741458d9a9f3cafd5a5a16eb1f7abe10bc15",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27600563281"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.20.0",
      "date": "2026-06-16T07:18:47.000Z",
      "commit": "b87f30eb2fa20b33d4040542c2d93c1243eae1ff",
      "fileid": "334fab90f44798d4d2a2ea5bcbe3ab46c904e3c8c2d550055bec6fc35ad1caa4",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27600563281"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.20.0",
      "date": "2026-06-16T07:19:30.000Z",
      "commit": "b87f30eb2fa20b33d4040542c2d93c1243eae1ff",
      "fileid": "b15d01dfce2be3d730bf872854f6b0be1af70a5e1ec3cfee21c3738b75066daa",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27600563281"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.20.0",
      "date": "2026-06-16T07:17:56.000Z",
      "commit": "b87f30eb2fa20b33d4040542c2d93c1243eae1ff",
      "fileid": "19fd36ccc471285260b852259c619d95ff2e41f73a805857e077a4a2aaedceb8",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27600563281"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.20.0",
      "date": "2026-06-16T07:17:56.000Z",
      "commit": "b87f30eb2fa20b33d4040542c2d93c1243eae1ff",
      "fileid": "264c7ce8f65b201eeaca4a203443a7f4dc5b8149d23d748ddb02c6eef0335fce",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27600563281"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.20.0",
      "date": "2026-06-16T07:18:00.000Z",
      "commit": "b87f30eb2fa20b33d4040542c2d93c1243eae1ff",
      "fileid": "c17b430d5cf495bb1281c698481b390b35e36d7cbb55db2fe264c4090087ee5c",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27600563281"
    }
  ]
}