{
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  "Title": "A Tool for Generic Cell Type Enrichment Analysis",
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  "Authors@R": "c(person(given = \"Almog\",\nfamily = \"Angel\",\nrole = c(\"aut\", \"cre\"),\nemail = \"almog.angel@campus.technion.ac.il\",\ncomment = c(ORCID = \"0009-0001-3297-6935\")),\nperson(given = \"Dvir\",\nfamily = \"Aran\",\nrole = \"aut\",\nemail = \"dviraran@technion.ac.il\",\ncomment = c(ORCID = \"0000-0001-6334-5039\")))",
  "Description": "xCell2 provides methods for cell type enrichment analysis\nusing cell type signatures. It includes three main functions -\n1. xCell2Train for training custom references objects from bulk\nor single-cell RNA-seq datasets. 2. xCell2Analysis for\nconducting the cell type enrichment analysis using the custom\nreference. 3. xCell2GetLineage for identifying dependencies\nbetween different cell types using ontology.",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:04:15 UTC",
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  "Author": "Almog Angel [aut, cre] (ORCID: <https://orcid.org/0009-0001-3297-6935>),\nDvir Aran [aut] (ORCID: <https://orcid.org/0000-0001-6334-5039>)",
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  "_exports": [
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    "getGenesUsed",
    "getParams",
    "getSignatures",
    "getSpillMat",
    "setDeps<-",
    "setGenesUsed<-",
    "setParams<-",
    "setSignatures<-",
    "setSpillMat<-",
    "xCell2Analysis",
    "xCell2GetLineage",
    "xCell2Train"
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  "_datasets": [
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      "name": "BlueprintEncode.xCell2Ref",
      "title": "Blueprint and ENCODE Projects Reference",
      "object": "BlueprintEncode.xCell2Ref",
      "file": "BlueprintEncode.xCell2Ref.rda",
      "class": [
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      "rows": 1000,
      "table": true,
      "tojson": true
    },
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      "object": "MouseRNAseqData.xCell2Ref",
      "file": "MouseRNAseqData.xCell2Ref.rda",
      "class": [
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      "table": false,
      "tojson": false
    },
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      "object": "PanCancer.xCell2Ref",
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      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "TabulaMurisBlood.xCell2Ref",
      "title": "Tabula Muris Blood Reference",
      "object": "TabulaMurisBlood.xCell2Ref",
      "file": "TabulaMurisBlood.xCell2Ref.rda",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "TabulaSapiensBlood.xCell2Ref",
      "title": "Tabula Sapiens Blood Reference",
      "object": "TabulaSapiensBlood.xCell2Ref",
      "file": "TabulaSapiensBlood.xCell2Ref.rda",
      "class": [
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      "table": false,
      "tojson": false
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    {
      "name": "TMECompendium.xCell2Ref",
      "title": "Tumor Microenvironment Compendium Reference",
      "object": "TMECompendium.xCell2Ref",
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      "table": false,
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  "_help": [
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      "page": "BlueprintEncode.xCell2Ref",
      "title": "Blueprint and ENCODE Projects Reference",
      "topics": [
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    {
      "page": "dependencies",
      "title": "Access Cell Type Dependencies",
      "topics": [
        "dependencies",
        "getDeps",
        "getDeps,xCell2Object-method",
        "setDeps<-",
        "setDeps<-,xCell2Object-method"
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    },
    {
      "page": "dice_demo_ref",
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      "topics": [
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      "topics": [
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      "title": "Access Genes Used",
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        "getGenesUsed",
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      "topics": [
        "PanCancer.xCell2Ref"
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    },
    {
      "page": "params",
      "title": "Access Transformation Parameters",
      "topics": [
        "getParams",
        "getParams,xCell2Object-method",
        "params",
        "setParams<-",
        "setParams<-,xCell2Object-method"
      ]
    },
    {
      "page": "signatures",
      "title": "Access Cell Type Signatures",
      "topics": [
        "getSignatures",
        "getSignatures,xCell2Object-method",
        "setSignatures<-",
        "setSignatures<-,xCell2Object-method",
        "signatures"
      ]
    },
    {
      "page": "spillMat",
      "title": "Access Spillover Matrix",
      "topics": [
        "getSpillMat",
        "getSpillMat,xCell2Object-method",
        "setSpillMat<-",
        "setSpillMat<-,xCell2Object-method",
        "spillMat"
      ]
    },
    {
      "page": "TabulaMurisBlood.xCell2Ref",
      "title": "Tabula Muris Blood Reference",
      "topics": [
        "TabulaMurisBlood.xCell2Ref"
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    {
      "page": "TabulaSapiensBlood.xCell2Ref",
      "title": "Tabula Sapiens Blood Reference",
      "topics": [
        "TabulaSapiensBlood.xCell2Ref"
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    },
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      "title": "Tumor Microenvironment Compendium Reference",
      "topics": [
        "TMECompendium.xCell2Ref"
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    },
    {
      "page": "xCell2Analysis",
      "title": "Perform Cell Type Enrichment Analysis",
      "topics": [
        "xCell2Analysis"
      ]
    },
    {
      "page": "xCell2GetLineage",
      "title": "Identify Cell Type Lineage Dependencies",
      "topics": [
        "xCell2GetLineage"
      ]
    },
    {
      "page": "xCell2Object-class",
      "title": "xCell2Object Class",
      "topics": [
        "xCell2Object-class"
      ]
    },
    {
      "page": "xCell2Train",
      "title": "Train Custom xCell2 Reference Object",
      "topics": [
        "xCell2Train"
      ]
    }
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  "_readme": "https://github.com/bioc/xCell2/raw/HEAD/README.md",
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    {
      "source": "xCell2-vignette.Rmd",
      "filename": "xCell2-vignette.html",
      "title": "xCell 2.0: Cell Type Enrichment Analysis",
      "author": "Almog Angel & Dvir Aran",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction to xCell 2.0 and Key Features",
        "Custom Reference Training",
        "Ontological Integration",
        "Spillover Correction",
        "Installation",
        "Creating a Custom Reference with xCell2Train",
        "Why Create a Custom Reference?",
        "Preparing the Input Data",
        "1. Reference Gene Expression Matrix",
        "2. Labels Data Frame",
        "Using SummarizedExperiment or SingleCellExperiment Objects",
        "Example: preparing the input data",
        "Assigning Cell Type Ontology (optional but recommended)",
        "When to Skip Ontology Assignment",
        "Assigning Ontologies",
        "Example: assigning cell type ontology",
        "Example: checking lineage relationships",
        "Generating the xCell2 Reference Object",
        "Key Parameters of xCell2Train",
        "Example: generating xCell2 reference object",
        "Sharing Your Custom xCell2 Reference Object",
        "Next Steps",
        "Using Pre-trained xCell2 References",
        "Available Pre-trained References",
        "Accessing Pre-trained References",
        "Choosing the Right Reference",
        "Calculating Cell Type Enrichment with xCell2Analysis",
        "Preparing the Input Data",
        "Key Parameters of xCell2Analysis",
        "Calculating Cell Type Enrichment",
        "Understanding Enrichment Scores",
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        "Normalizing Enrichment Scores by Tumor Purity",
        "Comparing Cellular Enrichment Across Conditions",
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