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  "Title": "Clustering Single-Cell Multimodal Omics Data with Joint Graph\nRegularized Single-Cell Kullback-Leibler Sparse Non-Negative\nMatrix Factorization",
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  "Date/Publication": "2024-06-10 07:25:17 UTC",
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    "CreateSickleJr",
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    "jrSiCKLSNMF",
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    "MinibatchDiagnosticPlot",
    "NormalizeCountMatrices",
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    "RunjrSiCKLSNMF",
    "SetLambdasandRegs",
    "SetWandHfromWHinitials",
    "SickleJr"
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    {
      "name": "SimData",
      "title": "A simulated dataset for use with jrSiCKLSNMF",
      "object": "SimData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "SimSickleJrSmall",
      "title": "A small SickleJr object containing a subset of data from the SimData data object. Contains the completed analysis from the 'Getting Started' vignette for a small subset of 10 cells with 150 genes and 700 peaks. The clusters derived from this dataset are not accurate; this dataset is intended for use with code examples.",
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      "class": [
        "SickleJr"
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      "table": false,
      "tojson": false
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      "title": "Add metadata to an object of class SickleJr",
      "topics": [
        "AddSickleJrMetadata"
      ]
    },
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      "topics": [
        "BuildKNNGraphLaplacians"
      ]
    },
    {
      "page": "BuildSNNGraphLaplacians",
      "title": "Build SNN graphs and generate their graph Laplacians",
      "topics": [
        "BuildSNNGraphLaplacians"
      ]
    },
    {
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      "title": "Calculate the UMAP for an object of class SickleJr",
      "topics": [
        "CalculateUMAPSickleJr"
      ]
    },
    {
      "page": "ClusterSickleJr",
      "title": "Cluster the \\mathbf{H} matrix",
      "topics": [
        "ClusterSickleJr"
      ]
    },
    {
      "page": "CreateSickleJr",
      "title": "Create an object of class SickleJr",
      "topics": [
        "CreateSickleJr"
      ]
    },
    {
      "page": "DetermineClusters",
      "title": "Perform clustering diagnostics",
      "topics": [
        "DetermineClusters"
      ]
    },
    {
      "page": "DetermineDFromIRLBA",
      "title": "Create elbow plots of the singular values derived from IRLBA to determine D for large datasets",
      "topics": [
        "DetermineDFromIRLBA"
      ]
    },
    {
      "page": "GenerateWmatricesandHmatrix",
      "title": "Generate the \\mathbf{W}^v matrices and \\mathbf{H} matrix",
      "topics": [
        "GenerateWmatricesandHmatrix"
      ]
    },
    {
      "page": "jrSiCKLSNMF",
      "title": "Run jrSiCKLSNMF outside of a SickleJr object",
      "topics": [
        "jrSiCKLSNMF"
      ]
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      "title": "Calculate the loss function in R",
      "topics": [
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      "topics": [
        "MinibatchDiagnosticPlot"
      ]
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    {
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      "title": "Normalize the count matrices and set whether to use the Poisson KL divergence or the Frobenius norm within each modality",
      "topics": [
        "NormalizeCountMatrices"
      ]
    },
    {
      "page": "PlotLossvsLatentFactors",
      "title": "Create plots to help determine the number of latent factors to use for jrSiCKLSNMF",
      "topics": [
        "PlotLossvsLatentFactors"
      ]
    },
    {
      "page": "PlotSickleJrUMAP",
      "title": "Generate UMAP plots for an object of class SickleJr",
      "topics": [
        "PlotSickleJrUMAP"
      ]
    },
    {
      "page": "RunjrSiCKLSNMF",
      "title": "Run jrSiCKLSNMF on an object of class SickleJr",
      "topics": [
        "RunjrSiCKLSNMF"
      ]
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        "SickleJr-class"
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        "SimData"
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