{
  "_id": "6a1afa581d7bb097a09fbf77",
  "Package": "SingleCellSignalR",
  "Title": "Cell Signalling Using Single-Cell RNA-seq or Proteomics Data",
  "Version": "2.3.0",
  "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 (L-R) interactions from\nsingle-cell expression (transcriptomics/proteomics) data.\nSingleCellSignalR v2 inferences rely on the statistical model\nwe introduced in the BulkSignalR package as well as the\noriginal SingleCellSignalR LR-score (both are available).\nSingleCellSignalR v2 can be regarded as a wrapper to\nBulkSignalR fundamental classes. This also enables v2 users to\nwork with any species, whereas only Mus musculus & Homo sapiens\nwere available before in SingleCellSignalR v1.",
  "URL": "https://github.com/jcolinge/SingleCellSignalR",
  "BugReports": "https://github.com/jcolinge/SingleCellSignalR/issues",
  "License": "CeCILL | file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "FALSE",
  "biocViews": "Network, RNASeq, Software, Proteomics, Transcriptomics,\nSingleCell, NetworkInference",
  "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 12:52:41 UTC",
  "RemoteUrl": "https://github.com/bioc/SingleCellSignalR",
  "RemoteRef": "HEAD",
  "RemoteSha": "8b72731b790c588bf5c00b37167b8ab1900fcf32",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:48:40 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": "c54c0746ba4e6e2b3375238b4138a02a",
  "_user": "bioc",
  "_type": "src",
  "_file": "SingleCellSignalR_2.3.0.tar.gz",
  "_fileid": "424d02a21febdbec7a8e37767eb64ba12e7ab8a3cfed17ad7b4ccb1d6cccb7d7",
  "_filesize": 332866,
  "_sha256": "424d02a21febdbec7a8e37767eb64ba12e7ab8a3cfed17ad7b4ccb1d6cccb7d7",
  "_created": "2026-05-30T09:48:40.000Z",
  "_published": "2026-05-30T14:55:20.078Z",
  "_jobs": [
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  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 6
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677004007",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/SingleCellSignalR",
  "_commit": {
    "id": "8b72731b790c588bf5c00b37167b8ab1900fcf32",
    "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": 1777380761
  },
  "_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": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "matrixTests",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "BulkSignalR",
      "role": "Imports"
    },
    {
      "package": "grid",
      "role": "Imports"
    },
    {
      "package": "ComplexHeatmap",
      "role": "Imports"
    },
    {
      "package": "circlize",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "markdown",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-39",
      "n": 1
    },
    {
      "week": "2025-40",
      "n": 1
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      "week": "2025-44",
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    {
      "week": "2025-45",
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    {
      "week": "2026-14",
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    {
      "week": "2026-16",
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    {
      "week": "2026-18",
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  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.3.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "2.2.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "network",
    "rnaseq",
    "software",
    "proteomics",
    "transcriptomics",
    "singlecell",
    "networkinference"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "loanedns",
      "count": 43,
      "uuid": 105852225
    },
    {
      "user": "zhefrench",
      "count": 36,
      "uuid": 14000664
    },
    {
      "user": "sca-ircm",
      "count": 30,
      "uuid": 52911489
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      "uuid": 65902924
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  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 571,
    "source": "https://www.bioconductor.org/packages/stats/bioc/SingleCellSignalR"
  },
  "_mentions": 7,
  "_devurl": "https://github.com/jcolinge/singlecellsignalr",
  "_searchresults": 49,
  "_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/SingleCellSignalR.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/jcolinge/singlecellsignalr",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "autocrines",
    "bsrdmComp",
    "cellNetBubblePlot",
    "cellNetHeatmap",
    "getAutocrines",
    "getParacrines",
    "infParamSC",
    "paracrines",
    "performInferences",
    "populations",
    "SCSRNet",
    "SCSRNoNet"
  ],
  "_datasets": [
    {
      "name": "example_dataset",
      "title": "An example of single-cell RNA-seq data set",
      "object": "example_dataset",
      "file": "example_dataset.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "genes",
        "TTCATTGTCGTACACA.1",
        "TAGGTTGAGCTCGCAC.1",
        "TTCAATCGTAGCGTCC.1",
        "AGGACTTGTCCAGCCA.1",
        "TTACTGTCAGTCGGAA.1",
        "GACTCAATCTGCGGAC.1",
        "CAGCAATTCACACGAT.1",
        "TGGTGATTCAATCCGA.1",
        "AGACTCACAATAACCC.1",
        "CCACACTCAACGCATT.1",
        "CTCAGAACAGCGTACC.1",
        "GACTGATCAGCATACT.1",
        "GCCGATGGTCGCCTAG.1",
        "CTACGGGGTCTTCATT.1",
        "ACCTACCCACGTATAC.1",
        "ATCATTCCAGTCACGC.1",
        "TCAGTTTTCATCCCGT.1",
        "GTGTGATCACACCTAA.1",
        "CACGTTCCAGTAGAAT.1",
        "TTCACGCCAGAACCGA.1",
        "GATGACTCAATAGTCC.1",
        "GACCAATGTCCATCTC.1",
        "GTTGTCCTCGGCTGGT.1",
        "ACCTACCCAACGTATC.1",
        "AAAGGTACAACTGGTT.1",
        "GAAGTAAAGGCCCAAA.1",
        "TCCCACATCAGGGTAG.1",
        "GGAGAACCAACCACAT.1",
        "GGCGTCAGTACCTTCC.1",
        "ATTCCCGCAAGCGCAA.1",
        "AGAAATGGTGAGTTTC.1",
        "GCCAGCATCGATGGAG.1",
        "AGCGTCGCAACTGCTA.1",
        "TGCAGGCCATCCTAAG.1",
        "TGACAGTTCGACGCTG.1",
        "CACAGATAGCAACAGC.1",
        "CCAATTTAGCGACTTT.1",
        "AATTTCCTCAAAGGAT.1",
        "GCAACCGCAGACCCGT.1",
        "AGACTCAAGCGGGTTA.1",
        "CTGCTCACAAGTGCAG.1",
        "GTATTTCCAGCTGTGC.1",
        "TCACACCCAGTGTGCC.1",
        "GCTTGGGAGCTGTACT.1",
        "TAGATCGTCGGACTGC.1",
        "GTCAGCGAGCACTCAT.1",
        "ATCTCTATCAAGAAAC.1",
        "TATTGGGAGCGACTTT.1",
        "CCTAAGAAGATGAAGG.1",
        "AGGAATAGTCAACATC.1",
        "GATAGCTCAGAGAGGG.1",
        "GCTTGGGTCGCCTCTA.1",
        "TGGGCGTTCGTGTTCC.1",
        "GTGTAACCACGACAGA.1",
        "CATTTCATCACTGGGC.1",
        "CTGTCGTGTGACCGTC.1",
        "ATCCATTCATGTCAGT.1",
        "CCGAACGGTTGTTGAC.1",
        "GTCGTAACAGTGCCTG.1",
        "GACTCAACACTAACGT.1",
        "TCCTCCCCACGTAACT.1",
        "GGGTTATGTTAGAAAC.1",
        "CACTAAGGTTGGCCGT.1",
        "GTAGGAGCAATCTCGA.1",
        "TACCTCGAGTTAGAAC.1",
        "AAGGAATTCGACCACG.1",
        "GTTCGCTTCAAAGACA.1",
        "AGTACCAAGCACTCCG.1",
        "ATTCTACTCTTACACT.1",
        "CTCATTAAGGTGCAGT.1",
        "TTTCACAAGAGGTATT.1",
        "CAACAGTCAACAAGTA.1",
        "TCGGGCACACCGCTAG.1",
        "CGCAGGTTCACAGTGT.1",
        "TGTTGAGAGATTGCGG.1",
        "CTTCAATTCGTGGACC.1",
        "ATGAGTCAGAGGCGGA.1",
        "AGCCAATTCGGCTTGG.1",
        "GGGCCATAGATCGCTT.1",
        "TGGAACTGTGTCTCCT.1",
        "AACCATGTCCGCGATG.1",
        "TGACCCTCACGAGAAC.1",
        "ACGATCACAGTTGGTT.1",
        "ATCAGGTGTTTACCAG.1",
        "CTGTAGAAGATGCAGC.1",
        "ATTCGTTGTACAGTAA.1",
        "AAACGCTGTGTGTACT.1",
        "TGCGGGTAGTGGATTA.1",
        "CGTAAGTTCCAACTGA.1",
        "AAAGTCCTCGGAACTT.1",
        "GTAGATCTCACATTGG.1",
        "AGCATCATCTTCGATT.1",
        "AAAGAACAGGATTCCT.1",
        "GGTTGTATCGACGCTG.1",
        "TGCATGAGTTGTACGT.1",
        "CTCCACAGTAAGCGGT.1",
        "CACGTGGGTTAAACCC.1",
        "TGTGTGATCGCTAGCG.1",
        "GCACATAGTAATTAGG.1",
        "TATATCCCAAGTAGTA.1",
        "GCGGATCCACTGTGTA.1",
        "TTGGGTAAGTCACAGG.1",
        "TGGGATTGTCGTCAGC.1",
        "TCCTGCAGTATCGTAC.1",
        "ACAACCAAGTTGAAGT.1",
        "CAACAGTGTGGCACTC.1",
        "CCGGTGAAGAGCATCG.1",
        "TAATCTCAGGTAGACC.1",
        "TCGCAGGCACAAGTTC.1",
        "TCGAAGTTCGTCCTCA.1",
        "ATGCATGAGACGCCAA.1",
        "TGGGATTCATGGAACG.1",
        "TAAGTCGCATTCATCT.1",
        "AGTCTCCTCAATCCGA.1",
        "GAGTCATCACAACGTT.1",
        "TAGATCGAGTAAGGGA.1",
        "CTTCCGACACCTCTGT.1",
        "GGAGGATTCGCTCATC.1",
        "TACGGGCGTTTGGAAA.1",
        "TCTTAGTAGAGAATCT.1",
        "TATGTTCCATAGTCGT.1",
        "ACCCTTGTCCAAAGGG.1",
        "GCATTAGTCATGGGAG.1",
        "GACCCTTAGAGAGTTT.1",
        "TCCACCAGTGGGTCAA.1",
        "GAGGCAACAATCGTCA.1",
        "CGGTCAGTCTCTGCCA.1",
        "GTGCTGGGTCCAGTTA.1",
        "ATGGGTTAGCCTCACG.1",
        "CCGATCTTCCTACGAA.1",
        "GTTGTAGGTTTAGTCG.1",
        "AGACCCGCATCGCCTT.1",
        "CTCATCGAGTGTTGAA.1",
        "TATTCCAAGCTCGTGC.1",
        "GACCTTCAGTCACAGG.1",
        "ACGTAACCACGATAGG.1",
        "CATTGTTTCTTGCGCT.1",
        "GAGGGTACACGCTATA.1",
        "CATCCACAGGCCACCT.1",
        "GAGTCTAAGCTGCCAC.1",
        "ACTTCCGAGTCGGCAA.1",
        "TGCACGGCAAATGGAT.1",
        "GTAGAGGGTACTCGCG.1",
        "CTTACCGTCACTAGCA.1",
        "TAACTTCGTAGTATAG.1",
        "CGAATTGAGTAATCCC.1",
        "GTACAGTCATTGCCTC.1",
        "GGGTGTCTCCAAACCA.1",
        "GCTACCTAGCTATCTG.1",
        "GTCACGGTCTGAGGCC.1",
        "TCTCAGCAGCGCCTTG.1",
        "GTTATGGCAATGCAAA.1",
        "CCTCAGTTCCATTTGT.1",
        "AAACCCAGTCTACACA.1",
        "ACTATCTTCGTCCTTG.1",
        "AAACGAACAGCTGTCG.1",
        "ATCATTCCAGCGGTCT.1",
        "GCTGAATAGGAACGAA.1",
        "TTGCTGCGTGCCGAAA.1",
        "GGTGGCTCACCCTAGG.1",
        "CTGGTCTAGATACTGA.1",
        "TGATCTTAGTTTCTTC.1",
        "CTCCTTTCAAATGGCG.1",
        "TACCTGCTCCCAGGCA.1",
        "TAAGCACCAGTCGAGA.1",
        "TGCGACGTCACTGCTC.1",
        "CGTAGTATCTGCGGGT.1",
        "GATGAGGAGAGAGCAA.1",
        "CAAGAGGGTGTGTCGC.1",
        "AGACAAATCGCGGTAC.1",
        "GTCTCACAGCTCACTA.1",
        "ACTGTCCCAAGCAATA.1",
        "CCGGTAGTCGCTACAA.1",
        "CACAGATAGCACGGAT.1",
        "GTTGAACTCGTCGCTT.1",
        "GTTCTATCACCTCTGT.1",
        "AACAGGGGTACTGACT.1",
        "TATTCCACATGTGCTA.1",
        "ACACCAACACTGATTG.1",
        "GGGTTTACATGCCGCA.1",
        "AGTACCAGTTATAGAG.1",
        "CCGGTAGTCCTGTAGA.1",
        "TGCGGCAGTCAAAGAT.1",
        "TTTGGAGCAACGGTAG.1",
        "TTCATGTAGATCACCT.1",
        "GTGATGTAGTGCGCTC.1",
        "GGAGATGTCGGACGTC.1",
        "TTAGTCTAGATTAGTG.1",
        "AGTAGTCTCTCAACGA.1",
        "GTCTCACGTCAAATCC.1",
        "CTCTGGTGTGAAAGTT.1",
        "AATAGAGAGAGGGTGG.1",
        "TGTGAGTAGTGGAATT.1",
        "GCGGAAAGTCTGATAC.1",
        "GCAGCCAAGTCCCAAT.1",
        "ATCATTCTCTGTTCAT.1",
        "TACACCCAGTGTTGTC.1",
        "TCGTCCAAGGGAGGAC.1",
        "GCTTGGGTCCTTTGAT.1",
        "CGTGCTTCAGTGCCTG.1",
        "CCTCAACTCGACCCAG.1",
        "AGGTCATCACCTGTCT.1",
        "TGTAACGGTTTGTGGT.1",
        "CTCCACAAGCTGTTAC.1",
        "ATCTCTAAGCGATTCT.1",
        "CGACAGCCAGACACAG.1",
        "TTGAGTGAGCACCGAA.1",
        "AGAGCCCTCCATCTCG.1",
        "GACTGATGTCTACACA.1",
        "GATAGAACACAATCTG.1",
        "TGATCTTCACCAAAGG.1",
        "TGCATGAGTAGTCACT.1",
        "ATACTTCGTAGACGGT.1",
        "ATCGGATAGTAGTGCG.1",
        "GAAACCTGTCTGCAAT.1",
        "ACCTGAAAGAAGCTGC.1",
        "GTTCCGTAGTCTCCTC.1",
        "TGTGCGGTCGTAACCA.1",
        "CAACAGTCAACATACC.1",
        "GTCCCATGTTCGGTCG.1",
        "GCTACCTTCCGCAAAT.1",
        "GTTTGGATCGGTCGGT.1",
        "ATGCCTCTCCTAGAGT.1",
        "TTCCAATAGTATGGCG.1",
        "ATTCCCGCACAATGTC.1",
        "CATCCCAGTGCACGCT.1",
        "TTCACCGGTGCCTGAC.1",
        "AGCTACAGTCAGGTGA.1",
        "TTACTGTGTACGGCAA.1",
        "GCCGATGCAATCGTCA.1",
        "AGTTAGCGTCGTATTG.1",
        "CGGGTGTAGTACAGCG.1",
        "CTCGAGGTCACCTTGC.1",
        "ACGATCAAGTCCCAAT.1",
        "TTACGCCGTTCAAACC.1",
        "GCCCGAATCCGGACTG.1",
        "TCTCAGCGTTGCGTAT.1",
        "AGTGTTGTCCAACCAA.1",
        "TTTCAGTCACGTGTGC.1",
        "TGTCAGAAGCCTGGAA.1",
        "TTCCTTCTCTCAATCT.1",
        "TGCCGAGTCCAGCACG.1",
        "TGGGAGATCTGCCCTA.1",
        "CGTTCTGAGCGAAACC.1",
        "TCAGCAATCATCGACA.1",
        "CATGCGGGTTCTGACA.1",
        "TGTGCGGTCCGAAATC.1",
        "AGTAGCTCATCGCTCT.1",
        "TTGGGTATCATCTGTT.1",
        "GCCTGTTAGAGGCCAT.1",
        "GCTTGGGCACTGCACG.1",
        "AGGTCTAAGTCATCGT.1",
        "TCAGTCCAGGCCTAAG.1",
        "GTTGAACAGACCAAGC.1",
        "GTCAAGTTCTGAGCAT.1",
        "GGATGTTAGTCATGGG.1",
        "CATTTCAAGTGTAGTA.1",
        "GTACAACAGTAACAGT.1",
        "ATTCCCGTCTTGCGCT.1",
        "GATCATGGTCAATCTG.1",
        "AGAAGCGAGGGTAGCT.1",
        "GGTAGAGAGTAAGCAT.1",
        "CTGCGAGTCTCCTACG.1",
        "CTTCTAAAGATTGAGT.1",
        "ACATTTCCAATGCAGG.1",
        "TTCTTCCTCATGCCGG.1",
        "GAGTGAGTCCTGATAG.1",
        "AGCCACGAGGCCCGTT.1",
        "ACGGGTCAGCGATGCA.1",
        "TATCAGGCATCCAATG.1",
        "AATCGACCAGGGAATC.1",
        "AAAGTGAGTTTGTTGG.1",
        "TCTACATGTGACAGCA.1",
        "GCAACCGAGCGCCTAC.1",
        "TGAGACTTCTGAGAGG.1",
        "GTAGGTTGTAGCTCGC.1",
        "ATCCGTCCAAAGGCGT.1",
        "CTACCTGGTTGGGTTT.1",
        "AGGACTTCACACACTA.1",
        "TTGTGGATCATTCATC.1",
        "GGTTAACCAGCCGTCA.1",
        "GAACACTTCTAGATCG.1",
        "TATCCTAGTAACGTTC.1",
        "TTTAGTCGTCCTACGG.1",
        "TGAGACTCAATGGCCC.1",
        "TGTGAGTCACATCATG.1",
        "GGCTGTGTCAAGATAG.1",
        "TCGTGGGAGGTGAGCT.1",
        "ATCCATTCACCACTGG.1",
        "GTAACCACAAGCGGAT.1",
        "ATGGGTTGTATCGCAT.1",
        "TGCTTCGTCGAGAAAT.1",
        "GTCAAACAGCGAGTAC.1",
        "TGACCCTTCCGTGGTG.1",
        "CGTTGGGAGGATCATA.1",
        "ATACCTTCACGGTAGA.1",
        "CATGCCTGTAACATAG.1",
        "TTGGGTAAGCAGAAAG.1",
        "CCACACTTCTTGGTGA.1",
        "ACGTCCTAGAACTTCC.1",
        "CTTACCGCATAACCCA.1",
        "TCAATTCCATACAGGG.1",
        "TGAGCATGTAACTTCG.1",
        "TAAGCGTAGTTGGACG.1",
        "AGTTCGACACTGGATT.1",
        "TTGGGTAGTGAATGAT.1",
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        "ATCACTTCAGTGTGGA.1",
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        "AGGTAGGTCTGCCTGT.1",
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        "TCTGGCTCACATCATG.1",
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