{
  "_id": "6a1e991c1d7bb097a0a6dc58",
  "Package": "BulkSignalR",
  "Type": "Package",
  "Title": "Infer Ligand-Receptor Interactions from bulk expression\n(transcriptomics/proteomics) data, or spatial transcriptomics",
  "Version": "1.5.0",
  "Authors@R": "c(\nperson(\"Jacques\",\"Colinge\",email=\"jacques.colinge@inserm.fr\",role=\"aut\",comment = c(ORCID = \"0000-0003-2466-4824\")),\nperson(\"Jean-Philippe\",\"Villemin\",email=\"jpvillemin@gmail.com\",role=\"cre\",comment = c(ORCID = \"0000-0002-1838-5880\")))",
  "Description": "Inference of ligand-receptor (LR) interactions from bulk\nexpression (transcriptomics/proteomics) data, or spatial\ntranscriptomics. BulkSignalR bases its inferences on the LRdb\ndatabase included in our other package, SingleCellSignalR\navailable from Bioconductor. It relies on a statistical model\nthat is specific to bulk data sets. Different visualization and\ndata summary functions are proposed to help navigating\nprediction results.",
  "URL": "https://github.com/jcolinge/BulkSignalR",
  "BugReports": "https://github.com/jcolinge/BulkSignalR/issues",
  "License": "CeCILL | file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "FALSE",
  "biocViews": "Network, RNASeq, Software, Proteomics, Transcriptomics,\nNetworkInference, Spatial",
  "Config/testthat/edition": "3",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libmagick++-dev gsfonts\nlibicu-dev libpng-dev libuv1-dev libxml2-dev libssl-dev perl\nlibx11-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:04:07 UTC",
  "RemoteUrl": "https://github.com/bioc/BulkSignalR",
  "RemoteRef": "HEAD",
  "RemoteSha": "ada5f6379d7eea20850787979aae5ee7a4f769b8",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-02 08:37:48 UTC",
    "User": "root"
  },
  "Author": "Jacques Colinge [aut] (ORCID: <https://orcid.org/0000-0003-2466-4824>),\nJean-Philippe Villemin [cre] (ORCID:\n<https://orcid.org/0000-0002-1838-5880>)",
  "Maintainer": "Jean-Philippe Villemin <jpvillemin@gmail.com>",
  "MD5sum": "b4ee13a3fe0dfb9337e1304474dc8e51",
  "_user": "bioc",
  "_type": "src",
  "_file": "BulkSignalR_1.5.0.tar.gz",
  "_fileid": "6b105e3acf4e71f980fd096453b233e0d00e8f3b8bab1b397cb51bfcf702f27c",
  "_filesize": 4420767,
  "_sha256": "6b105e3acf4e71f980fd096453b233e0d00e8f3b8bab1b397cb51bfcf702f27c",
  "_created": "2026-06-02T08:37:48.000Z",
  "_published": "2026-06-02T08:49:32.920Z",
  "_jobs": [
    {
      "job": 79032035212,
      "time": 271,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7353002457"
    },
    {
      "job": 79032035208,
      "time": 553,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7353100550"
    },
    {
      "job": 79032035221,
      "time": 573,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7353107305"
    },
    {
      "job": 79032035273,
      "time": 465,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7353078509"
    },
    {
      "job": 79032035211,
      "time": 360,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7353043139"
    },
    {
      "job": 79030667564,
      "time": 482,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7352908503"
    },
    {
      "job": 79032035183,
      "time": 207,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7352980177"
    },
    {
      "job": 79032035189,
      "time": 621,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7353123934"
    },
    {
      "job": 79032035153,
      "time": 604,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7353117567"
    },
    {
      "job": 79032035279,
      "time": 552,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7353100321"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 5
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26808078975",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/BulkSignalR",
  "_commit": {
    "id": "ada5f6379d7eea20850787979aae5ee7a4f769b8",
    "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": 1777381447
  },
  "_maintainer": {
    "name": "Jean-Philippe Villemin",
    "email": "jpvillemin@gmail.com",
    "login": "zhefrench",
    "twitter": "@ZheFrench",
    "description": "Bioinformatician - Institute of Cancer Research of Montpellier  : Cancer Genomics / Alternative Splicing / Epigenetic",
    "uuid": 14000664,
    "orcid": "0000-0002-1838-5880"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.5",
      "role": "Depends"
    },
    {
      "package": "BiocFileCache",
      "role": "Imports"
    },
    {
      "package": "httr2",
      "role": "Imports"
    },
    {
      "package": "RCurl",
      "role": "Imports"
    },
    {
      "package": "cli",
      "role": "Imports"
    },
    {
      "package": "curl",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "glmnet",
      "role": "Imports"
    },
    {
      "package": "ggalluvial",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "gridExtra",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Imports"
    },
    {
      "package": "Rtsne",
      "role": "Imports"
    },
    {
      "package": "ggrepel",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "multtest",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "orthogene",
      "role": "Imports"
    },
    {
      "package": "stabledist",
      "role": "Imports"
    },
    {
      "package": "circlize",
      "version": ">= 0.4.14",
      "role": "Imports"
    },
    {
      "package": "ComplexHeatmap",
      "version": ">= 2.0.0",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "RANN",
      "role": "Imports"
    },
    {
      "package": "SpatialExperiment",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "tools",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "markdown",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "STexampleData",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "codetools",
      "role": "Suggests"
    },
    {
      "package": "Matrix",
      "role": "Suggests"
    },
    {
      "package": "lattice",
      "role": "Suggests"
    },
    {
      "package": "cluster",
      "role": "Suggests"
    },
    {
      "package": "survival",
      "role": "Suggests"
    },
    {
      "package": "MASS",
      "role": "Suggests"
    },
    {
      "package": "nlme",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-31",
      "n": 5
    },
    {
      "week": "2025-39",
      "n": 4
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2025-45",
      "n": 1
    },
    {
      "week": "2026-09",
      "n": 2
    },
    {
      "week": "2026-14",
      "n": 2
    },
    {
      "week": "2026-17",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.5.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.4.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "network",
    "rnaseq",
    "software",
    "proteomics",
    "transcriptomics",
    "networkinference",
    "spatial"
  ],
  "_stars": 27,
  "_contributors": [
    {
      "user": "zhefrench",
      "count": 106,
      "uuid": 14000664
    },
    {
      "user": "jcolinge",
      "count": 92,
      "uuid": 65902924
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 452,
    "source": "https://www.bioconductor.org/packages/stats/bioc/BulkSignalR"
  },
  "_devurl": "https://github.com/jcolinge/bulksignalr",
  "_searchresults": 16,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/BulkSignalR.html",
    "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",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/jcolinge/bulksignalr",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "addClusterComp",
    "alluvialPlot",
    "assignCellTypesToInteractions",
    "BSRClusterComp",
    "BSRDataModel",
    "BSRDataModelComp",
    "BSRInference",
    "BSRInferenceComp",
    "BSRSignature",
    "BSRSignatureComp",
    "bubblePlotPathwaysLR",
    "cacheClear",
    "cacheInfo",
    "cacheVersion",
    "cellTypeFrequency",
    "cellularNetwork",
    "cellularNetworkTable",
    "chordDiagramLR",
    "coerce",
    "colClusterA",
    "colClusterB",
    "comparison",
    "comparisonName",
    "convertToHuman",
    "createResources",
    "differentialStats",
    "findOrthoGenes",
    "generateSpatialPlots",
    "getLRIntracellNetwork",
    "getLRNetwork",
    "getPathwayStats",
    "getResource",
    "inferenceParameters",
    "initialOrganism",
    "initialOrthologs",
    "learnParameters",
    "ligands",
    "logTransformed",
    "LRinter",
    "LRinterScore",
    "LRinterShort",
    "maxLigandSpatialCounts",
    "mu",
    "ncounts",
    "normalization",
    "parameters",
    "pathways",
    "receptors",
    "reduceToBestPathway",
    "reduceToLigand",
    "reduceToPathway",
    "reduceToReceptor",
    "relateToGeneSet",
    "removeClusterComp",
    "rescoreInference",
    "resetLRdb",
    "resetNetwork",
    "resetPathways",
    "resetToInitialOrganism",
    "scoreLRGeneSignatures",
    "scoreSignatures",
    "separatedLRPlot",
    "signatureHeatmaps",
    "simpleHeatmap",
    "smoothSpatialCounts",
    "sourceComparisonName",
    "spatialAssociation",
    "spatialAssociationPlot",
    "spatialDiversityPlot",
    "spatialIndexPlot",
    "spatialPlot",
    "summarizedCellularNetwork",
    "tgCorr",
    "tgExpr",
    "tgGenes",
    "tgLogFC",
    "tgPval",
    "updateInference"
  ],
  "_datasets": [
    {
      "name": "annotation.spa",
      "title": "A skinny data frame used in the spatial workflow",
      "object": "annotation.spa",
      "file": "annotation.spa.rda",
      "class": [
        "DFrame"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "bodyMap.mouse",
      "title": "Mouse transcriptoms across tissues",
      "object": "bodyMap.mouse",
      "file": "bodyMap.mouse.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "mBr_M_844",
        "mBr_M_796",
        "mBr_M_780",
        "mBr_M_846",
        "mLi_M_847",
        "mLi_M_797",
        "mLi_M_781",
        "mLi_M_845"
      ],
      "rows": 24543,
      "table": true,
      "tojson": true
    },
    {
      "name": "bsrdm",
      "title": "A skinny BSRDataModel object related to sdc.",
      "object": "bsrdm",
      "file": "bsrdm.comp.rda",
      "class": [
        "BSRDataModel"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "bsrdm.comp",
      "title": "A skinny BSRDataModelComp object related to sdc.",
      "object": "bsrdm.comp",
      "file": "bsrdm.comp.rda",
      "class": [
        "BSRDataModelComp"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "bsrdm.spa",
      "title": "A skinny BSRDataModel object related to a spatial data set",
      "object": "bsrdm.spa",
      "file": "bsrdm.spa.rda",
      "class": [
        "BSRDataModel"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "bsrinf",
      "title": "A skinny BSRInference object related to sdc.",
      "object": "bsrinf",
      "file": "bsrinf.comp.rda",
      "class": [
        "BSRInference"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "bsrinf.comp",
      "title": "A skinny BSRInferenceComp object related to sdc.",
      "object": "bsrinf.comp",
      "file": "bsrinf.comp.rda",
      "class": [
        "BSRInferenceComp"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "bsrinf.mouse",
      "title": "A skinny BSRInference object related to bodyMap.mouse",
      "object": "bsrinf.mouse",
      "file": "bsrinf.mouse.rda",
      "class": [
        "BSRInference"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "bsrinf.spa",
      "title": "A skinny BSR-inference object related to spatial data set",
      "object": "bsrinf.spa",
      "file": "bsrinf.spa.rda",
      "class": [
        "BSRInference"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "immune.signatures",
      "title": "Immune cell gene signatures",
      "object": "immune.signatures",
      "file": "immune.signatures.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "gene",
        "signature"
      ],
      "rows": 1541,
      "table": true,
      "tojson": true
    },
    {
      "name": "ortholog.dict",
      "title": "A skinny data frame used in the mouse workflow",
      "object": "ortholog.dict",
      "file": "ortholog.dict.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Gene.name"
      ],
      "rows": 4572,
      "table": true,
      "tojson": true
    },
    {
      "name": "p.EMT",
      "title": "Partial EMT gene signature",
      "object": "p.EMT",
      "file": "p.EMT.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "gene"
      ],
      "rows": 100,
      "table": true,
      "tojson": true
    },
    {
      "name": "sdc",
      "title": "Salivary duct carcinoma transcriptoms",
      "object": "sdc",
      "file": "sdc.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "SDC16",
        "SDC15",
        "SDC14",
        "SDC13",
        "SDC12",
        "SDC11",
        "SDC10",
        "SDC9",
        "SDC8",
        "SDC7",
        "SDC6",
        "SDC5",
        "SDC4",
        "SDC3",
        "SDC2",
        "SDC1",
        "SDC17",
        "SDC19",
        "SDC20",
        "N20",
        "SDC21",
        "SDC22",
        "N22",
        "SDC23",
        "SDC24",
        "SDC25"
      ],
      "rows": 19764,
      "table": true,
      "tojson": true
    },
    {
      "name": "tme.signatures",
      "title": "Tumor microenvironment gene signatures",
      "object": "tme.signatures",
      "file": "tme.signatures.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "gene",
        "signature"
      ],
      "rows": 213,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "dot-formatPathwaysFromGmt",
      "title": "Transform gmt file to data frame",
      "topics": [
        ".formatPathwaysFromGmt"
      ]
    },
    {
      "page": "dot-formatPathwaysFromJson",
      "title": "Format a data frame according to json input",
      "topics": [
        ".formatPathwaysFromJson"
      ]
    },
    {
      "page": "dot-formatPathwaysFromTxt",
      "title": "Read dataframe from txt file",
      "topics": [
        ".formatPathwaysFromTxt"
      ]
    },
    {
      "page": "dot-testCacheFiles",
      "title": "Check there is a well formatted cache",
      "topics": [
        ".testCacheFiles"
      ]
    },
    {
      "page": "dot-testRemoteServer",
      "title": "Check whether the reference DB server is up",
      "topics": [
        ".testRemoteServer"
      ]
    },
    {
      "page": "addClusterComp",
      "title": "Add a comparison between two clusters of samples",
      "topics": [
        "addClusterComp",
        "addClusterComp,BSRDataModelComp-method"
      ]
    },
    {
      "page": "alluvialPlot",
      "title": "Alluvial plot",
      "topics": [
        "alluvialPlot"
      ]
    },
    {
      "page": "annotation.spa",
      "title": "A skinny data frame used in the spatial workflow",
      "topics": [
        "annotation.spa"
      ]
    },
    {
      "page": "assignCellTypesToInteractions",
      "title": "Assign cell types to L-R interactions",
      "topics": [
        "assignCellTypesToInteractions"
      ]
    },
    {
      "page": "bodyMap.mouse",
      "title": "Mouse transcriptoms across tissues",
      "topics": [
        "bodyMap.mouse"
      ]
    },
    {
      "page": "BSRClusterComp",
      "title": "Definition of the comparison between two clusters of samples",
      "topics": [
        "BSRClusterComp"
      ]
    },
    {
      "page": "BSRClusterComp-class",
      "title": "BulkSignalR Cluster Comparison Object",
      "topics": [
        "BSRClusterComp-class"
      ]
    },
    {
      "page": "BSRDataModel",
      "title": "Constructor of the BSRDataModel class",
      "topics": [
        "BSRDataModel"
      ]
    },
    {
      "page": "BSRDataModel-class",
      "title": "BulkSignalR Data Model Object",
      "topics": [
        "BSRDataModel-class"
      ]
    },
    {
      "page": "BSRDataModelComp",
      "title": "Constructor of the BSRDataModelComp class",
      "topics": [
        "BSRDataModelComp"
      ]
    },
    {
      "page": "BSRDataModelComp-class",
      "title": "BulkSignalR Data Model Compare Object",
      "topics": [
        "BSRDataModelComp-class"
      ]
    },
    {
      "page": "bsrdm",
      "title": "A skinny BSRDataModel object related to sdc.",
      "topics": [
        "bsrdm"
      ]
    },
    {
      "page": "bsrdm.comp",
      "title": "A skinny BSRDataModelComp object related to sdc.",
      "topics": [
        "bsrdm.comp"
      ]
    },
    {
      "page": "bsrdm.spa",
      "title": "A skinny BSRDataModel object related to a spatial data set",
      "topics": [
        "bsrdm.spa"
      ]
    },
    {
      "page": "bsrinf",
      "title": "A skinny BSRInference object related to sdc.",
      "topics": [
        "bsrinf"
      ]
    },
    {
      "page": "bsrinf.comp",
      "title": "A skinny BSRInferenceComp object related to sdc.",
      "topics": [
        "bsrinf.comp"
      ]
    },
    {
      "page": "bsrinf.mouse",
      "title": "A skinny BSRInference object related to bodyMap.mouse",
      "topics": [
        "bsrinf.mouse"
      ]
    },
    {
      "page": "bsrinf.spa",
      "title": "A skinny BSR-inference object related to spatial data set",
      "topics": [
        "bsrinf.spa"
      ]
    },
    {
      "page": "BSRInference",
      "title": "Inference of ligand-receptor interactions",
      "topics": [
        "BSRInference"
      ]
    },
    {
      "page": "BSRInference-class",
      "title": "BulkSignalR Inference Object",
      "topics": [
        "BSRInference-class"
      ]
    },
    {
      "page": "BSRInferenceComp",
      "title": "Inference of ligand-receptor interactions based on regulation",
      "topics": [
        "BSRInferenceComp"
      ]
    },
    {
      "page": "BSRInferenceComp-class",
      "title": "BulkSignalR cluster comparison-based inference object",
      "topics": [
        "BSRInferenceComp-class"
      ]
    },
    {
      "page": "BSRSignature",
      "title": "Extract gene signatures of LR pair activity",
      "topics": [
        "BSRSignature"
      ]
    },
    {
      "page": "BSRSignature-class",
      "title": "BulkSignalR ligand-receptor signature Object",
      "topics": [
        "BSRSignature-class"
      ]
    },
    {
      "page": "BSRSignatureComp",
      "title": "Extract gene signatures of LR pair activity",
      "topics": [
        "BSRSignatureComp"
      ]
    },
    {
      "page": "BSRSignatureComp-class",
      "title": "BulkSignalR ligand-receptor signature object for cluster comparisons",
      "topics": [
        "BSRSignatureComp-class"
      ]
    },
    {
      "page": "bubblePlotPathwaysLR",
      "title": "Bubble Plot to explore LR & Pathways",
      "topics": [
        "bubblePlotPathwaysLR"
      ]
    },
    {
      "page": "cacheClear",
      "title": "Delete cache content.",
      "topics": [
        "cacheClear"
      ]
    },
    {
      "page": "cacheInfo",
      "title": "Get cache content information.",
      "topics": [
        "cacheInfo"
      ]
    },
    {
      "page": "cacheVersion",
      "title": "Check whether remote resource files have been changed.",
      "topics": [
        "cacheVersion"
      ]
    },
    {
      "page": "cellTypeFrequency",
      "title": "Cell type frequencies in relations to gene sets",
      "topics": [
        "cellTypeFrequency"
      ]
    },
    {
      "page": "cellularNetwork",
      "title": "Build a cellular network",
      "topics": [
        "cellularNetwork"
      ]
    },
    {
      "page": "cellularNetworkTable",
      "title": "Build a table describing a cellular network",
      "topics": [
        "cellularNetworkTable"
      ]
    },
    {
      "page": "chordDiagramLR",
      "title": "Chord Diagram of LR interactions with correlations",
      "topics": [
        "chordDiagramLR"
      ]
    },
    {
      "page": "coerce",
      "title": "Convert BSRDataModel to BSRDataModelComp",
      "topics": [
        "coerce",
        "coerce,BSRDataModel,BSRDataModelComp-method"
      ]
    },
    {
      "page": "colClusterA",
      "title": "Cluster A columns accessor",
      "topics": [
        "colClusterA",
        "colClusterA,BSRClusterComp-method"
      ]
    },
    {
      "page": "colClusterB",
      "title": "Cluster B columns accessor",
      "topics": [
        "colClusterB",
        "colClusterB,BSRClusterComp-method"
      ]
    },
    {
      "page": "comparison",
      "title": "Comparisons list accessor",
      "topics": [
        "comparison",
        "comparison,BSRDataModelComp-method"
      ]
    },
    {
      "page": "comparisonName",
      "title": "Comparison name accessor",
      "topics": [
        "comparisonName",
        "comparisonName,BSRInferenceComp-method",
        "comparisonName,BSRSignatureComp-method"
      ]
    },
    {
      "page": "convertToHuman",
      "title": "Transpose to Human Gene Names",
      "topics": [
        "convertToHuman"
      ]
    },
    {
      "page": "createResources",
      "title": "Create all resources",
      "topics": [
        "createResources"
      ]
    },
    {
      "page": "differentialStats",
      "title": "Cluster comparison statistics accessor",
      "topics": [
        "differentialStats",
        "differentialStats,BSRClusterComp-method"
      ]
    },
    {
      "page": "findOrthoGenes",
      "title": "Orthologs Gene Names",
      "topics": [
        "findOrthoGenes"
      ]
    },
    {
      "page": "generateSpatialPlots",
      "title": "Generate L-R interaction score spatial plots in a folder",
      "topics": [
        "generateSpatialPlots"
      ]
    },
    {
      "page": "getLRIntracellNetwork",
      "title": "Generate a ligand-receptor-downstream signaling network",
      "topics": [
        "getLRIntracellNetwork"
      ]
    },
    {
      "page": "getLRNetwork",
      "title": "Generate a ligand-receptor network",
      "topics": [
        "getLRNetwork"
      ]
    },
    {
      "page": "getPathwayStats",
      "title": "Basic statistics about hit pathways",
      "topics": [
        "getPathwayStats",
        "getPathwayStats,BSRInference-method"
      ]
    },
    {
      "page": "getResource",
      "title": "Get resources from the cache",
      "topics": [
        "getResource"
      ]
    },
    {
      "page": "immune.signatures",
      "title": "Immune cell gene signatures",
      "topics": [
        "immune.signatures"
      ]
    },
    {
      "page": "inferenceParameters",
      "title": "Inference parameters accessor",
      "topics": [
        "inferenceParameters",
        "inferenceParameters,BSRInference-method"
      ]
    },
    {
      "page": "initialOrganism",
      "title": "organism accessor",
      "topics": [
        "initialOrganism",
        "initialOrganism,BSRDataModel-method"
      ]
    },
    {
      "page": "initialOrthologs",
      "title": "Model parameter accessor",
      "topics": [
        "initialOrthologs",
        "initialOrthologs,BSRDataModel-method"
      ]
    },
    {
      "page": "learnParameters",
      "title": "Training of BulkSignalR model parameters",
      "topics": [
        "learnParameters",
        "learnParameters,BSRDataModel-method"
      ]
    },
    {
      "page": "ligands",
      "title": "ligands accessor",
      "topics": [
        "ligands",
        "ligands,BSRInference-method",
        "ligands,BSRSignature-method"
      ]
    },
    {
      "page": "logTransformed",
      "title": "log.transformed accessor",
      "topics": [
        "logTransformed",
        "logTransformed,BSRDataModel-method"
      ]
    },
    {
      "page": "LRinter",
      "title": "LRinter accessor",
      "topics": [
        "LRinter",
        "LRinter,BSRInference-method"
      ]
    },
    {
      "page": "LRinterScore",
      "title": "Simplified LRinter accessor with focus on the LR-score",
      "topics": [
        "LRinterScore",
        "LRinterScore,BSRInferenceComp-method"
      ]
    },
    {
      "page": "LRinterShort",
      "title": "Simplified LRinter accessor reporting the essential columns",
      "topics": [
        "LRinterShort",
        "LRinterShort,BSRInference-method",
        "LRinterShort,BSRInferenceComp-method"
      ]
    },
    {
      "page": "maxLigandSpatialCounts",
      "title": "Get maximal ligand expression at nearby locations",
      "topics": [
        "maxLigandSpatialCounts"
      ]
    },
    {
      "page": "mu",
      "title": "Mu accessor",
      "topics": [
        "mu",
        "mu,BSRDataModelComp-method"
      ]
    },
    {
      "page": "ncounts",
      "title": "Normalized count matrix accessor",
      "topics": [
        "ncounts",
        "ncounts,BSRDataModel-method"
      ]
    },
    {
      "page": "normalization",
      "title": "Normalization accessor",
      "topics": [
        "normalization",
        "normalization,BSRDataModel-method"
      ]
    },
    {
      "page": "ortholog.dict",
      "title": "A skinny data frame used in the mouse workflow",
      "topics": [
        "ortholog.dict"
      ]
    },
    {
      "page": "p.EMT",
      "title": "Partial EMT gene signature",
      "topics": [
        "p.EMT"
      ]
    },
    {
      "page": "parameters",
      "title": "Model parameter accessor",
      "topics": [
        "parameters",
        "parameters,BSRDataModel-method"
      ]
    },
    {
      "page": "pathways",
      "title": "pathways accessor",
      "topics": [
        "pathways",
        "pathways,BSRSignature-method"
      ]
    },
    {
      "page": "receptors",
      "title": "receptors accessor",
      "topics": [
        "receptors",
        "receptors,BSRInference-method",
        "receptors,BSRSignature-method"
      ]
    },
    {
      "page": "reduceToBestPathway",
      "title": "Keep one pathway per ligand-receptor pair",
      "topics": [
        "reduceToBestPathway",
        "reduceToBestPathway,BSRInference-method",
        "reduceToBestPathway,BSRInferenceComp-method"
      ]
    },
    {
      "page": "reduceToLigand",
      "title": "Aggregate the receptors of a same ligand",
      "topics": [
        "reduceToLigand",
        "reduceToLigand,BSRInference-method",
        "reduceToLigand,BSRInferenceComp-method"
      ]
    },
    {
      "page": "reduceToPathway",
      "title": "Aggregate ligands and receptors at the pathway level",
      "topics": [
        "reduceToPathway",
        "reduceToPathway,BSRInference-method",
        "reduceToPathway,BSRInferenceComp-method"
      ]
    },
    {
      "page": "reduceToReceptor",
      "title": "Aggregate the ligands of a same receptor",
      "topics": [
        "reduceToReceptor",
        "reduceToReceptor,BSRInference-method",
        "reduceToReceptor,BSRInferenceComp-method"
      ]
    },
    {
      "page": "relateToGeneSet",
      "title": "Relate ligands to a gene set",
      "topics": [
        "relateToGeneSet"
      ]
    },
    {
      "page": "removeClusterComp",
      "title": "Remove a comparison from a BSRDataModelComp object.",
      "topics": [
        "removeClusterComp",
        "removeClusterComp,BSRDataModelComp-method"
      ]
    },
    {
      "page": "rescoreInference",
      "title": "Inference re-scoring",
      "topics": [
        "rescoreInference",
        "rescoreInference,BSRInference-method",
        "rescoreInference,BSRInferenceComp-method"
      ]
    },
    {
      "page": "resetLRdb",
      "title": "Modify LRdb database",
      "topics": [
        "resetLRdb"
      ]
    },
    {
      "page": "resetNetwork",
      "title": "Import a refernce network of your own",
      "topics": [
        "resetNetwork"
      ]
    },
    {
      "page": "resetPathways",
      "title": "Import pathways from a file or data frame",
      "topics": [
        "resetPathways"
      ]
    },
    {
      "page": "resetToInitialOrganism",
      "title": "Reset gene names to initial organism provided in the first instance",
      "topics": [
        "resetToInitialOrganism",
        "resetToInitialOrganism,BSRInference-method"
      ]
    },
    {
      "page": "scoreLRGeneSignatures",
      "title": "Score ligand-receptor gene signatures",
      "topics": [
        "scoreLRGeneSignatures",
        "scoreLRGeneSignatures,BSRDataModel-method",
        "scoreLRGeneSignatures,BSRDataModelComp-method"
      ]
    },
    {
      "page": "scoreSignatures",
      "title": "Generic gene signature scoring",
      "topics": [
        "scoreSignatures"
      ]
    },
    {
      "page": "sdc",
      "title": "Salivary duct carcinoma transcriptoms",
      "topics": [
        "sdc"
      ]
    },
    {
      "page": "separatedLRPlot",
      "title": "Generate separated plots for a L-R interaction",
      "topics": [
        "separatedLRPlot"
      ]
    },
    {
      "page": "signatureHeatmaps",
      "title": "Heatmap function to dissect one pathway signature",
      "topics": [
        "signatureHeatmaps"
      ]
    },
    {
      "page": "simpleHeatmap",
      "title": "Heatmap function for LR scores",
      "topics": [
        "simpleHeatmap"
      ]
    },
    {
      "page": "smoothSpatialCounts",
      "title": "Smooth spatial expression data",
      "topics": [
        "smoothSpatialCounts"
      ]
    },
    {
      "page": "sourceComparisonName",
      "title": "Source comparison name accessor",
      "topics": [
        "sourceComparisonName",
        "sourceComparisonName,BSRInferenceComp-method"
      ]
    },
    {
      "page": "spatialAssociation",
      "title": "Statistical association of scores with area labels",
      "topics": [
        "spatialAssociation"
      ]
    },
    {
      "page": "spatialAssociationPlot",
      "title": "Heatmap plot of association of scores with area labels",
      "topics": [
        "spatialAssociationPlot"
      ]
    },
    {
      "page": "spatialDiversityPlot",
      "title": "2D-projection of spatial score distributions",
      "topics": [
        "spatialDiversityPlot"
      ]
    },
    {
      "page": "spatialIndexPlot",
      "title": "Generate a visual index of spatial score distributions",
      "topics": [
        "spatialIndexPlot"
      ]
    },
    {
      "page": "spatialPlot",
      "title": "L-R interaction score spatial display",
      "topics": [
        "spatialPlot"
      ]
    },
    {
      "page": "summarizedCellularNetwork",
      "title": "Build a summary cellular network",
      "topics": [
        "summarizedCellularNetwork"
      ]
    },
    {
      "page": "tgCorr",
      "title": "Target gene correlations accessor",
      "topics": [
        "tgCorr",
        "tgCorr,BSRInference-method",
        "tgCorr,BSRSignature-method"
      ]
    },
    {
      "page": "tgExpr",
      "title": "Target gene expression accessor",
      "topics": [
        "tgExpr",
        "tgExpr,BSRInferenceComp-method",
        "tgExpr,BSRSignatureComp-method"
      ]
    },
    {
      "page": "tgGenes",
      "title": "Target genes accessor",
      "topics": [
        "tgGenes",
        "tgGenes,BSRInference-method",
        "tgGenes,BSRSignature-method"
      ]
    },
    {
      "page": "tgLogFC",
      "title": "Target gene logFC accessor",
      "topics": [
        "tgLogFC",
        "tgLogFC,BSRInferenceComp-method",
        "tgLogFC,BSRSignatureComp-method"
      ]
    },
    {
      "page": "tgPval",
      "title": "Target gene P-values accessor",
      "topics": [
        "tgPval",
        "tgPval,BSRInferenceComp-method",
        "tgPval,BSRSignatureComp-method"
      ]
    },
    {
      "page": "tme.signatures",
      "title": "Tumor microenvironment gene signatures",
      "topics": [
        "tme.signatures"
      ]
    },
    {
      "page": "updateInference",
      "title": "Inference updating",
      "topics": [
        "updateInference",
        "updateInference,BSRInferenceComp-method"
      ]
    }
  ],
  "_pkglogo": "https://github.com/bioc/BulkSignalR/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/bioc/BulkSignalR/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "ape",
    "aplot",
    "askpass",
    "babelgene",
    "backports",
    "base64enc",
    "Biobase",
    "BiocFileCache",
    "BiocGenerics",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "boot",
    "broom",
    "bslib",
    "cachem",
    "car",
    "carData",
    "circlize",
    "cli",
    "clipr",
    "clue",
    "cluster",
    "codetools",
    "colorspace",
    "ComplexHeatmap",
    "corrplot",
    "cowplot",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "Deriv",
    "digest",
    "doBy",
    "doParallel",
    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "fontBitstreamVera",
    "fontLiberation",
    "fontquiver",
    "foreach",
    "forecast",
    "Formula",
    "fracdiff",
    "fs",
    "gdtools",
    "generics",
    "GenomicRanges",
    "GetoptLong",
    "ggalluvial",
    "ggfun",
    "ggiraph",
    "ggplot2",
    "ggplotify",
    "ggpubr",
    "ggrepel",
    "ggsci",
    "ggsignif",
    "ggtree",
    "glmnet",
    "GlobalOptions",
    "glue",
    "gprofiler2",
    "gridExtra",
    "gridGraphics",
    "gtable",
    "highr",
    "hms",
    "homologene",
    "htmltools",
    "htmlwidgets",
    "httr",
    "httr2",
    "igraph",
    "IRanges",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "lme4",
    "lmtest",
    "magick",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "MatrixModels",
    "matrixStats",
    "memoise",
    "mgcv",
    "microbenchmark",
    "mime",
    "minqa",
    "modelr",
    "multtest",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "openssl",
    "orthogene",
    "otel",
    "patchwork",
    "pbkrtest",
    "pillar",
    "pkgconfig",
    "plotly",
    "plyr",
    "png",
    "polynom",
    "prettyunits",
    "progress",
    "promises",
    "purrr",
    "quantreg",
    "R.cache",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "RANN",
    "rappdirs",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "RCurl",
    "Rdpack",
    "readr",
    "reformulas",
    "repmis",
    "rjson",
    "rlang",
    "rmarkdown",
    "RSQLite",
    "rstatix",
    "Rtsne",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "shape",
    "SingleCellExperiment",
    "SparseArray",
    "SparseM",
    "SpatialExperiment",
    "stabledist",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sys",
    "systemfonts",
    "tibble",
    "tidyr",
    "tidyselect",
    "tidytree",
    "timeDate",
    "tinytex",
    "treeio",
    "tzdb",
    "urca",
    "utf8",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr",
    "xfun",
    "XVector",
    "yaml",
    "yulab.utils",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "BulkSignalR-Configure.Rmd",
      "filename": "BulkSignalR-Configure.html",
      "title": "BulkSignalR : Inference of ligand-receptor interactions from bulk data or spatial transcriptomics",
      "author": "Jean-Philippe Villemin, Jacques Colinge",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Configure local cache and hidden environment variables",
        "Session Information"
      ],
      "created": "2025-09-26 18:24:50",
      "modified": "2025-09-26 18:24:50",
      "commits": 1
    },
    {
      "source": "BulkSignalR-Differential.Rmd",
      "filename": "BulkSignalR-Differential.html",
      "title": "BulkSignalR : Inference of ligand-receptor interactions from bulk data or spatial transcriptomics",
      "author": "Jean-Philippe Villemin, Jacques Colinge",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Cluster-based differential analysis",
        "Technical notes",
        "Session Information"
      ],
      "created": "2023-08-14 13:08:41",
      "modified": "2025-07-29 14:49:29",
      "commits": 16
    },
    {
      "source": "BulkSignalR-Main.Rmd",
      "filename": "BulkSignalR-Main.html",
      "title": "BulkSignalR : Inference of ligand-receptor interactions from bulk data or spatial transcriptomics",
      "author": "Jean-Philippe Villemin, Jacques Colinge",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "What is it for?",
        "Starting point",
        "How does it work?",
        "Parallel mode settings",
        "First Example",
        "Loading the data",
        "Building a BSRDataModel object",
        "Building a BSRInference object",
        "Reduction strategies",
        "Reducing a BSRInference object to pathways",
        "Reducing a BSRInference object to the best pathways",
        "Reducing to ligands or receptors",
        "Combined reductions",
        "Building a BSRSignature object",
        "Scoring by ligand-receptor",
        "Scoring by pathway",
        "Other visualization utilities",
        "Heatmap of ligand-receptor-target genes expression",
        "AlluvialPlot",
        "BubblePlot",
        "Chordiagram",
        "Network Analysis",
        "Non-human data",
        "Spatial Transcriptomics",
        "Acknowledgements",
        "Session Information"
      ],
      "created": "2023-08-14 13:08:41",
      "modified": "2025-09-26 18:24:50",
      "commits": 19
    }
  ],
  "_score": 7.1917862475822,
  "_indexed": true,
  "_nocasepkg": "bulksignalr",
  "_universes": [
    "bioc",
    "zhefrench",
    "jcolinge"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.5.0",
      "date": "2026-06-02T08:42:35.000Z",
      "distro": "noble",
      "commit": "ada5f6379d7eea20850787979aae5ee7a4f769b8",
      "fileid": "87e71051d59959f63191ea7178a95c1df34832d4290250ee3f0394101b7e9c53",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808078975"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.5.0",
      "date": "2026-06-02T08:42:20.000Z",
      "distro": "noble",
      "commit": "ada5f6379d7eea20850787979aae5ee7a4f769b8",
      "fileid": "dd4058714161f4bf2c70d0ec0380f974247efea461d2c26893913bfc8a62d04e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808078975"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.5.0",
      "date": "2026-06-02T08:41:31.000Z",
      "commit": "ada5f6379d7eea20850787979aae5ee7a4f769b8",
      "fileid": "73ee200c1b1f369f55564afd5248a92a30c17b91e2389363f210ea15fec3e257",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808078975"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.5.0",
      "date": "2026-06-02T08:40:53.000Z",
      "commit": "ada5f6379d7eea20850787979aae5ee7a4f769b8",
      "fileid": "11cdaf24800efb28749c00e0bcc08f150bb1dbb23ba91b65a02d8f3a2bae394d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808078975"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.5.0",
      "date": "2026-06-02T08:42:14.000Z",
      "commit": "ada5f6379d7eea20850787979aae5ee7a4f769b8",
      "fileid": "c0e37332952f3785ea61acaf92310a70a58e2610efe54ffbc6ede871b15c0468",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808078975"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.5.0",
      "date": "2026-06-02T08:42:28.000Z",
      "commit": "ada5f6379d7eea20850787979aae5ee7a4f769b8",
      "fileid": "afa40803db806e0b1f605606ab588d8441ad314c888194adac03bb85e9811638",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808078975"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.5.0",
      "date": "2026-06-02T08:42:31.000Z",
      "commit": "ada5f6379d7eea20850787979aae5ee7a4f769b8",
      "fileid": "10534310f47211f8610f763ddbe34d5c08778f90dd029696246c536a205b1c11",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808078975"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.5.0",
      "date": "2026-06-02T08:42:13.000Z",
      "commit": "ada5f6379d7eea20850787979aae5ee7a4f769b8",
      "fileid": "824db551924f4839eacd1a2b189c4bf523397e2b7e1dcb082180e594ec297a2e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26808078975"
    }
  ]
}