{
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  "Package": "HIPPO",
  "Type": "Package",
  "Title": "Heterogeneity-Induced Pre-Processing tOol",
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  "Authors@R": "c(\nperson(given = 'Tae', family = 'Kim', email = 'tk382@uchicago.edu', role = c('aut', 'cre')),\nperson(given = 'Mengjie', family = 'Chen', email = 'mengjiechen@uchicago.edu', role = 'aut')\n)",
  "Description": "For scRNA-seq data, it selects features and clusters the\ncells simultaneously for single-cell UMI data. It has a novel\nfeature selection method using the zero inflation instead of\ngene variance, and computationally faster than other existing\nmethods since it only relies on PCA+Kmeans rather than\ngraph-clustering or consensus clustering.",
  "License": "GPL (>=2)",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/tk382/HIPPO",
  "BugReports": "https://github.com/tk382/HIPPO/issues",
  "RoxygenNote": "7.1.0",
  "biocViews": "Sequencing, SingleCell, GeneExpression,\nDifferentialExpression, Clustering",
  "Config/pak/sysreqs": "libicu-dev libpng-dev libssl-dev python3 zlib1g-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:52:13 UTC",
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  "RemoteRef": "RELEASE_3_23",
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  "NeedsCompilation": "no",
  "Packaged": {
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    "User": "root"
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  "Author": "Tae Kim [aut, cre],\nMengjie Chen [aut]",
  "Maintainer": "Tae Kim <tk382@uchicago.edu>",
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  "_contributors": [
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    "pois_prob_zero",
    "preprocess_heterogeneous",
    "preprocess_homogeneous",
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        "ensg"
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      "tojson": true
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      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": false
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      "title": "re-export magrittr pipe operator",
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      ]
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      "topics": [
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      "title": "Access data from SCE object",
      "topics": [
        "get_data_from_sce"
      ]
    },
    {
      "page": "get_hippo",
      "title": "Access hippo object from SingleCellExperiment object.",
      "topics": [
        "get_hippo"
      ]
    },
    {
      "page": "get_hippo_diffexp",
      "title": "Return hippo_diffexp object",
      "topics": [
        "get_hippo_diffexp"
      ]
    },
    {
      "page": "hippo",
      "title": "HIPPO's hierarchical clustering",
      "topics": [
        "hippo"
      ]
    },
    {
      "page": "hippo_diagnostic_plot",
      "title": "Conduct feature selection by computing test statistics for each gene",
      "topics": [
        "hippo_diagnostic_plot"
      ]
    },
    {
      "page": "hippo_diffexp",
      "title": "HIPPO's differential expression",
      "topics": [
        "hippo_diffexp"
      ]
    },
    {
      "page": "hippo_dimension_reduction",
      "title": "compute t-SNE or umap of each round of HIPPO",
      "topics": [
        "hippo_dimension_reduction"
      ]
    },
    {
      "page": "hippo_feature_heatmap",
      "title": "HIPPO's feature heatmap",
      "topics": [
        "hippo_feature_heatmap"
      ]
    },
    {
      "page": "hippo_pca_plot",
      "title": "visualize each round of hippo through t-SNE",
      "topics": [
        "hippo_pca_plot"
      ]
    },
    {
      "page": "hippo_tsne_plot",
      "title": "visualize each round of hippo through t-SNE",
      "topics": [
        "hippo_tsne_plot"
      ]
    },
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      "page": "hippo_umap_plot",
      "title": "visualize each round of hippo through UMAP",
      "topics": [
        "hippo_umap_plot"
      ]
    },
    {
      "page": "nb_prob_zero",
      "title": "Expected zero proportion under Negative Binomial",
      "topics": [
        "nb_prob_zero"
      ]
    },
    {
      "page": "pois_prob_zero",
      "title": "Expected zero proportion under Poisson",
      "topics": [
        "pois_prob_zero"
      ]
    },
    {
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      "title": "Preprocess UMI data without cell label so that each row contains information about each gene",
      "topics": [
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    },
    {
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      "title": "Preprocess UMI data with inferred or known labels",
      "topics": [
        "preprocess_homogeneous"
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    },
    {
      "page": "toydata",
      "title": "A sample single cell sequencing data subsetted from Zheng2017",
      "topics": [
        "toydata"
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    },
    {
      "page": "zero_proportion_plot",
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      "topics": [
        "zero_proportion_plot"
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    },
    {
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      "title": "Expected zero proportion under Negative Binomial",
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        "Differential Expression Example"
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      "created": "2019-12-30 02:10:28",
      "modified": "2020-03-26 15:57:20",
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