{
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  "Package": "CHETAH",
  "Title": "Fast and accurate scRNA-seq cell type identification",
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  "Version": "1.28.0",
  "Date": "2025-10-14",
  "Authors@R": "c(person(\"Jurrian\", \"de Kanter\", email = \"jurriandekanter@gmail.com\",  role = c(\"aut\", \"cre\")),\nperson(\"Philip\", \"Lijnzaad\", email = \"p.lijnzaad@prinsesmaximacentrum.nl\", role = c(\"aut\")))",
  "Description": "CHETAH (CHaracterization of cEll Types Aided by\nHierarchical classification) is an accurate, selective and fast\nscRNA-seq classifier. Classification is guided by a reference\ndataset, preferentially also a scRNA-seq dataset. By\nhierarchical clustering of the reference data, CHETAH creates a\nclassification tree that enables a step-wise, top-to-bottom\nclassification. Using a novel stopping rule, CHETAH classifies\nthe input cells to the cell types of the references and to\n\"intermediate types\": more general classifications that ended\nin an intermediate node of the tree.",
  "License": "file LICENSE",
  "Encoding": "UTF-8",
  "biocViews": "Classification, RNASeq, SingleCell, Clustering,\nGeneExpression, ImmunoOncology",
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  "URL": "https://github.com/jdekanter/CHETAH",
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  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:58:40 UTC",
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    "CHETAHshiny",
    "Classify",
    "ClassifyReference",
    "CorrelateReference",
    "PlotCHETAH",
    "PlotTree",
    "PlotTSNE",
    "RenameBelowNode"
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      "name": "headneck_ref",
      "title": "A SingleCellExperiment with celltypes in the \"celltypes\" colData. A subset of the Head-Neck data from Puram et al. (2017) Cancer Cell.",
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      "table": false,
      "tojson": false
    },
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      "name": "input_mel",
      "title": "A SingleCellExperiment on which CHEATHclassifier is run using the 'headneck_ref' It holds subset of the Melanoma data, from Tirosh et al. (2016), Science.",
      "object": "input_mel",
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    {
      "page": "CHETAHclassifier",
      "title": "Identification of cell types aided by hierarchical clustering",
      "topics": [
        "CHETAHclassifier"
      ]
    },
    {
      "page": "CHETAHshiny",
      "title": "Launch a web page to interactively go trough the classification",
      "topics": [
        "CHETAHshiny"
      ]
    },
    {
      "page": "Classify",
      "title": "(Re)classify after running 'CHETAHclassifier' using a confidence threshold NOTE: In case of bulk reference profiles: only the correlations will be used, as the data does not allow for profile or confidence scores to be calculated.",
      "topics": [
        "Classify"
      ]
    },
    {
      "page": "ClassifyReference",
      "title": "Use a reference dataset to classify itself. A good reference should have almost no mixture between reference cells.",
      "topics": [
        "ClassifyReference"
      ]
    },
    {
      "page": "CorrelateReference",
      "title": "Correlate all reference profiles to each other using differentially expressed genes.",
      "topics": [
        "CorrelateReference"
      ]
    },
    {
      "page": "headneck_ref",
      "title": "A SingleCellExperiment with celltypes in the \"celltypes\" colData. A subset of the Head-Neck data from Puram et al. (2017) Cancer Cell.",
      "topics": [
        "headneck_ref"
      ]
    },
    {
      "page": "input_mel",
      "title": "A SingleCellExperiment on which CHEATHclassifier is run using the 'headneck_ref' It holds subset of the Melanoma data, from Tirosh et al. (2016), Science.",
      "topics": [
        "input_mel"
      ]
    },
    {
      "page": "PlotCHETAH",
      "title": "Plot the CHETAH classification on 2D visulization like t-SNE + the corresponding classification tree, colored with the same colors",
      "topics": [
        "PlotCHETAH"
      ]
    },
    {
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      "title": "Plots the chetah classification tree with nodes numbered",
      "topics": [
        "PlotTree"
      ]
    },
    {
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      "title": "Plots a variable on a t-SNE",
      "topics": [
        "PlotTSNE"
      ]
    },
    {
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      "title": "In the CHETAH classification, replace the name of a Node and all the names of the final and intermediate types under that Node.",
      "topics": [
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      ]
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      "filename": "CHETAH_introduction.html",
      "title": "Introduction to the CHETAH package",
      "author": "Jurrian de Kanter",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "At a glance",
        "Some background",
        "Installation",
        "Preparing your data",
        "Required data",
        "To prepare the data from the package's internal data, run:",
        "The input data: a Matrix",
        "The reduced dimensions of the input cells: 2 column matrix",
        "The reference data: a Matrix",
        "The cell types of the reference: a named character vector",
        "The names of the cell types correspond with the colnames of the reference counts:",
        "Running CHETAH",
        "The output",
        "Standard plots",
        "CHETAHshiny",
        "Changing classification",
        "Confidence score",
        "Renaming types",
        "Creating a reference",
        "Step 0: Obtain a reference.",
        "Step 1: good reference characteristics",
        "Step 1: normalization",
        "Step 2: discaring of house-keeping genes",
        "Step 3: Reference QC",
        "CorrelateReference",
        "ClassifyReference",
        "Optimizing the classification"
      ],
      "created": "2019-02-17 20:04:35",
      "modified": "2022-07-08 14:57:47",
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