{
  "_id": "6a1bef921d7bb097a0a21ff0",
  "Package": "UMI4Cats",
  "Title": "UMI4Cats: Processing, analysis and visualization of UMI-4C\nchromatin contact data",
  "Version": "1.23.0",
  "Authors@R": "c(\nperson(given = \"Mireia\",\nfamily = \"Ramos-Rodriguez\",\nrole = c(\"aut\", \"cre\"),\nemail = \"mireiarr9@gmail.com\",\ncomment = c(ORCID = \"0000-0001-8083-2445\")),\nperson(given = \"Marc\",\nfamily = \"Subirana-Granes\",\nrole = c(\"aut\"),\nemail = \"marc.subirana@upf.edu\"),\nperson(given = \"Lorenzo\",\nfamily = \"Pasquali\",\nrole = c(\"aut\"),\nemail = \"lorenzo.pasquali@upf.edu\"))",
  "URL": "https://github.com/Pasquali-lab/UMI4Cats",
  "Description": "UMI-4C is a technique that allows characterization of 3D\nchromatin interactions with a bait of interest, taking\nadvantage of a sonication step to produce unique molecular\nidentifiers (UMIs) that help remove duplication bias, thus\nallowing a better differential comparsion of chromatin\ninteractions between conditions. This package allows processing\nof UMI-4C data, starting from FastQ files provided by the\nsequencing facility. It provides two statistical methods for\ndetecting differential contacts and includes a visualization\nfunction to plot integrated information from a UMI-4C assay.",
  "BugReports": "https://github.com/Pasquali-lab/UMI4Cats/issues",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "biocViews": "QualityControl, Preprocessing, Alignment, Normalization,\nVisualization, Sequencing, Coverage",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:53:22 UTC",
  "RemoteUrl": "https://github.com/bioc/UMI4Cats",
  "RemoteRef": "HEAD",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-31 07:00:54 UTC",
    "User": "root"
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  "Author": "Mireia Ramos-Rodriguez [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-8083-2445>),\nMarc Subirana-Granes [aut],\nLorenzo Pasquali [aut]",
  "Maintainer": "Mireia Ramos-Rodriguez <mireiarr9@gmail.com>",
  "MD5sum": "38a2fd1ae3eb2d587115e630fe22f3db",
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  "_type": "src",
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  "_created": "2026-05-31T07:00:54.000Z",
  "_published": "2026-05-31T08:21:38.688Z",
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    "chromatin-interaction",
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  "_homeurl": "https://github.com/pasquali-lab/umi4cats",
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  "_exports": [
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    "addGrouping",
    "alignmentUMI4C",
    "bait",
    "callInteractions",
    "combineUMI4C",
    "contactsUMI4C",
    "counterUMI4C",
    "createGeneAnnotation",
    "darken",
    "demultiplexFastq",
    "dgram",
    "dgram<-",
    "differentialNbinomWaldTestUMI4C",
    "digestGenome",
    "downloadUMI4CexampleData",
    "fisherUMI4C",
    "getSignInteractions",
    "getViewpointCoordinates",
    "groupsUMI4C",
    "groupsUMI4C<-",
    "makeUMI4C",
    "makeWindowFragments",
    "plotDifferential",
    "plotDomainogram",
    "plotGenes",
    "plotInteractions",
    "plotInteractionsUMI4C",
    "plotTrend",
    "plotUMI4C",
    "prepUMI4C",
    "resultsUMI4C",
    "splitUMI4C",
    "statsUMI4C",
    "theme",
    "themeXblank",
    "themeXYblank",
    "themeYblank",
    "trend",
    "UMI4C",
    "waldUMI4C"
  ],
  "_datasets": [
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      "name": "ex_ciita_umi4c",
      "title": "Contacts with CIITA promoter",
      "object": "ex_ciita_umi4c",
      "file": "ex_ciita_umi4c.rda",
      "class": [
        "UMI4C"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "dot-getCache",
      "title": "Get BiocFileCache object",
      "topics": [
        ".getCache"
      ]
    },
    {
      "page": "dot-getSummaryBam",
      "title": "Summarize BAM file",
      "topics": [
        ".getSummaryBam"
      ]
    },
    {
      "page": "dot-singleAlignmentUMI4C",
      "title": "Align split fastq file",
      "topics": [
        ".singleAlignmentUMI4C"
      ]
    },
    {
      "page": "dot-singleCounterUMI4C",
      "title": "Count UMIs for a given bam file.",
      "topics": [
        ".singleCounterUMI4C"
      ]
    },
    {
      "page": "dot-singlePrepUMI4C",
      "title": "Prepar fastq files at a given barcode.",
      "topics": [
        ".singlePrepUMI4C"
      ]
    },
    {
      "page": "dot-singleSplitUMI4C",
      "title": "Split fastq files at a given restriction site.",
      "topics": [
        ".singleSplitUMI4C"
      ]
    },
    {
      "page": "dot-smoothMonotone",
      "title": "Monotone smoothing of the VST counts",
      "topics": [
        ".smoothMonotone"
      ]
    },
    {
      "page": "addGrouping",
      "title": "Add grouping of UMI-4C samples",
      "topics": [
        "addGrouping"
      ]
    },
    {
      "page": "addStepping",
      "title": "Add stepping for plotting genes",
      "topics": [
        "addStepping"
      ]
    },
    {
      "page": "alignmentUMI4C",
      "title": "UMI4C alignment",
      "topics": [
        "alignmentUMI4C"
      ]
    },
    {
      "page": "calculateAdaptativeTrend",
      "title": "Adaptative smoothing of normalized trend",
      "topics": [
        "calculateAdaptativeTrend"
      ]
    },
    {
      "page": "calculateDomainogram",
      "title": "Create Domainogram",
      "topics": [
        "calculateDomainogram"
      ]
    },
    {
      "page": "callInteractions",
      "title": "Call significant interactions",
      "topics": [
        "callInteractions"
      ]
    },
    {
      "page": "combineUMI4C",
      "title": "Combine UMI4C fragments",
      "topics": [
        "combineUMI4C"
      ]
    },
    {
      "page": "contactsUMI4C",
      "title": "UMI4C Contacts Processing",
      "topics": [
        "contactsUMI4C"
      ]
    },
    {
      "page": "counterUMI4C",
      "title": "UMI counting",
      "topics": [
        "counterUMI4C"
      ]
    },
    {
      "page": "createGeneAnnotation",
      "title": "Create gene annotation object",
      "topics": [
        "createGeneAnnotation"
      ]
    },
    {
      "page": "createStatsTable",
      "title": "Create stats table",
      "topics": [
        "createStatsTable"
      ]
    },
    {
      "page": "darken",
      "title": "Darken colors",
      "topics": [
        "darken"
      ]
    },
    {
      "page": "dds2UMI4C",
      "title": "DDS object to UMI4Cats object.",
      "topics": [
        "dds2UMI4C"
      ]
    },
    {
      "page": "demultiplexFastq",
      "title": "Demultiplex FASTQ files using fastq-multx",
      "topics": [
        "demultiplexFastq"
      ]
    },
    {
      "page": "UMI4C-methods",
      "title": "UMI4C class methods",
      "topics": [
        "bait",
        "bait,UMI4C-method",
        "dgram",
        "dgram,UMI4C-method",
        "dgram<-",
        "dgram<-,UMI4C-method",
        "groupsUMI4C",
        "groupsUMI4C,UMI4C-method",
        "groupsUMI4C<-",
        "groupsUMI4C<-,UMI4C-method",
        "resultsUMI4C",
        "resultsUMI4C,UMI4C-method",
        "trend",
        "trend,UMI4C-method",
        "UMI4C-methods"
      ]
    },
    {
      "page": "differentialNbinomWaldTestUMI4C",
      "title": "Differential UMI4C contacts using DESeq2 Wald Test",
      "topics": [
        "differentialNbinomWaldTestUMI4C"
      ]
    },
    {
      "page": "digestGenome",
      "title": "Digest reference genome",
      "topics": [
        "digestGenome"
      ]
    },
    {
      "page": "downloadUMI4CexampleData",
      "title": "Download UMI4Cats example datasets",
      "topics": [
        "downloadUMI4CexampleData"
      ]
    },
    {
      "page": "ex_ciita_umi4c",
      "title": "Contacts with CIITA promoter",
      "topics": [
        "ex_ciita_umi4c"
      ]
    },
    {
      "page": "fisherUMI4C",
      "title": "Differential UMI4C contacts using Fisher's Exact test",
      "topics": [
        "fisherUMI4C"
      ]
    },
    {
      "page": "formatPlotsUMI4C",
      "title": "Format plots for UMI4C",
      "topics": [
        "formatPlotsUMI4C"
      ]
    },
    {
      "page": "geoMeanCoordinates",
      "title": "Get geometric mean of given coordinates",
      "topics": [
        "geoMeanCoordinates"
      ]
    },
    {
      "page": "getColors",
      "title": "Get default colors",
      "topics": [
        "getColors"
      ]
    },
    {
      "page": "getFactors",
      "title": "Get factors fro plotting",
      "topics": [
        "getFactors"
      ]
    },
    {
      "page": "getNormalizationMatrix",
      "title": "Get normalization matrix",
      "topics": [
        "getNormalizationMatrix"
      ]
    },
    {
      "page": "getSignInteractions",
      "title": "Get significant interactions from a GRangesList",
      "topics": [
        "getSignInteractions"
      ]
    },
    {
      "page": "getViewpointCoordinates",
      "title": "Get viewpoint coordinates",
      "topics": [
        "getViewpointCoordinates"
      ]
    },
    {
      "page": "groupSamplesUMI4C",
      "title": "Group UMI4C samples",
      "topics": [
        "groupSamplesUMI4C"
      ]
    },
    {
      "page": "makeWindowFragments",
      "title": "Make windows merging restriction fragments",
      "topics": [
        "makeWindowFragments"
      ]
    },
    {
      "page": "nbinomWaldTestUMI4C",
      "title": "Differential UMI4C contacts using DESeq2 Wald Test",
      "topics": [
        "nbinomWaldTestUMI4C"
      ]
    },
    {
      "page": "plotDifferential",
      "title": "Plot differential contacts",
      "topics": [
        "plotDifferential"
      ]
    },
    {
      "page": "plotDomainogram",
      "title": "Plot domainogram",
      "topics": [
        "plotDomainogram"
      ]
    },
    {
      "page": "plotGenes",
      "title": "Plot genes",
      "topics": [
        "plotGenes"
      ]
    },
    {
      "page": "plotInteractions",
      "title": "Plot interactions",
      "topics": [
        "plotInteractions"
      ]
    },
    {
      "page": "plotInteractionsUMI4C",
      "title": "Plot Interactions UMI4C",
      "topics": [
        "plotInteractionsUMI4C"
      ]
    },
    {
      "page": "plotTrend",
      "title": "Plot adaptative smoothen trend",
      "topics": [
        "plotTrend"
      ]
    },
    {
      "page": "plotUMI4C",
      "title": "Plot UMI4C data",
      "topics": [
        "plotUMI4C"
      ]
    },
    {
      "page": "prepUMI4C",
      "title": "Prepare UMI4C data",
      "topics": [
        "prepUMI4C"
      ]
    },
    {
      "page": "smoothMonotoneUMI4C",
      "title": "Monotone smoothing of the DDS object VST counts",
      "topics": [
        "smoothMonotoneUMI4C"
      ]
    },
    {
      "page": "splitUMI4C",
      "title": "Split UMI4C reads",
      "topics": [
        "splitUMI4C"
      ]
    },
    {
      "page": "statsUMI4C",
      "title": "Statistics UMI4C",
      "topics": [
        "statsUMI4C"
      ]
    },
    {
      "page": "theme",
      "title": "Theme",
      "topics": [
        "theme"
      ]
    },
    {
      "page": "themeXblank",
      "title": "Theme X blank",
      "topics": [
        "themeXblank"
      ]
    },
    {
      "page": "themeXYblank",
      "title": "Theme Y blank",
      "topics": [
        "themeXYblank"
      ]
    },
    {
      "page": "themeYblank",
      "title": "Theme Y blank",
      "topics": [
        "themeYblank"
      ]
    },
    {
      "page": "UMI4C",
      "title": "UMI4C-class",
      "topics": [
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      "source": "UMI4Cats.Rmd",
      "filename": "UMI4Cats.html",
      "title": "Analyzing UMI-4C data with UMI4Cats",
      "author": "Mireia Ramos-Rodríguez and Marc Subirana-Granés",
      "engine": "knitr::rmarkdown",
      "headings": [
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        "Overview of the package",
        "About the experimental design",
        "About the example datasets",
        "Quick start",
        "Preparing necessary files",
        "Demultiplexing FastQ files containing multiple baits",
        "Reference genome digestion",
        "Processing UMI-4C FASTQ files",
        "Quality control measures",
        "Loading UMI-4C data into R",
        "Build the UMI4C object",
        "Accessing UMI4C object information",
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        "Methods",
        "Obtaining significant interactions",
        "Differential analysis",
        "Differential Analysis using DESeq2",
        "Differential analysis using Fisher's Exact Test",
        "Retrieve differential analysis results",
        "Visualizing UMI-4C contact data",
        "Session Information",
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      "created": "2020-06-12 09:02:35",
      "modified": "2025-10-21 10:59:01",
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