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  "Title": "Simplification of scRNA-seq data by merging together similar\ncells",
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    "supercell_FindMarkers",
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    "supercell_GeneGenePlot",
    "supercell_merge",
    "supercell_mergeGE",
    "supercell_plot",
    "supercell_plot_GE",
    "supercell_plot_tSNE",
    "supercell_plot_UMAP",
    "supercell_prcomp",
    "supercell_purity",
    "supercell_rescale",
    "supercell_silhouette",
    "supercell_tSNE",
    "supercell_UMAP",
    "supercell_VlnPlot"
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      "title": "Cancer cell lines dataset",
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      "class": [
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      "table": false,
      "tojson": false
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      "title": "Pancreatic cell dataset",
      "object": "pancreas",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
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    {
      "page": "anndata_2_supercell",
      "title": "Convert Anndata metacell object (Metacell-2 or SEACells) to Super-cell like object",
      "topics": [
        "anndata_2_supercell"
      ]
    },
    {
      "page": "build_knn_graph",
      "title": "Build kNN graph",
      "topics": [
        "build_knn_graph"
      ]
    },
    {
      "page": "build_knn_graph_nn2",
      "title": "Build kNN graph using RANN::nn2 (used in '\"build_knn_graph\"')",
      "topics": [
        "build_knn_graph_nn2"
      ]
    },
    {
      "page": "cell_lines",
      "title": "Cancer cell lines dataset",
      "topics": [
        "cell_lines"
      ]
    },
    {
      "page": "knn_graph_from_dist",
      "title": "Build kNN graph from distance (used in '\"build_knn_graph\"')",
      "topics": [
        "knn_graph_from_dist"
      ]
    },
    {
      "page": "metacell2_anndata_2_supercell",
      "title": "Convert Metacells (Metacell-2) to Super-cell like object",
      "topics": [
        "metacell2_anndata_2_supercell"
      ]
    },
    {
      "page": "pancreas",
      "title": "Pancreatic cell dataset",
      "topics": [
        "pancreas"
      ]
    },
    {
      "page": "sc_mixing_score",
      "title": "Compute mixing of single-cells within supercell",
      "topics": [
        "sc_mixing_score"
      ]
    },
    {
      "page": "SCimplify",
      "title": "Detection of metacells with the SuperCell approach",
      "topics": [
        "SCimplify"
      ]
    },
    {
      "page": "SCimplify_for_velocity",
      "title": "Construct super-cells from spliced and un-spliced matrices",
      "topics": [
        "SCimplify_for_velocity"
      ]
    },
    {
      "page": "SCimplify_from_embedding",
      "title": "Detection of metacells with the SuperCell approach from low dim representation",
      "topics": [
        "SCimplify_from_embedding"
      ]
    },
    {
      "page": "supercell_2_sce",
      "title": "Super-cells to SingleCellExperiment object",
      "topics": [
        "supercell_2_sce"
      ]
    },
    {
      "page": "supercell_2_Seurat",
      "title": "Super-cells to Seurat object",
      "topics": [
        "supercell_2_Seurat"
      ]
    },
    {
      "page": "supercell_assign",
      "title": "Assign super-cells to the most aboundant cluster",
      "topics": [
        "supercell_assign"
      ]
    },
    {
      "page": "supercell_cluster",
      "title": "Cluster super-cell data",
      "topics": [
        "supercell_cluster"
      ]
    },
    {
      "page": "supercell_DimPlot",
      "title": "Plot metacell 2D plot (PCA, UMAP, tSNE etc)",
      "topics": [
        "supercell_DimPlot"
      ]
    },
    {
      "page": "supercell_estimate_velocity",
      "title": "Run RNAvelocity for super-cells (slightly modified from gene.relative.velocity.estimates) Not yet adjusted for super-cell size (not sample-weighted)",
      "topics": [
        "supercell_estimate_velocity"
      ]
    },
    {
      "page": "supercell_FindAllMarkers",
      "title": "Differential expression analysis of supep-cell data. Most of the parameters are the same as in Seurat FindAllMarkers (for simplicity)",
      "topics": [
        "supercell_FindAllMarkers"
      ]
    },
    {
      "page": "supercell_FindMarkers",
      "title": "Differential expression analysis of supep-cell data. Most of the parameters are the same as in Seurat FindMarkers (for simplicity)",
      "topics": [
        "supercell_FindMarkers"
      ]
    },
    {
      "page": "supercell_GE",
      "title": "Simplification of scRNA-seq dataset",
      "topics": [
        "supercell_GE"
      ]
    },
    {
      "page": "supercell_GE_idx",
      "title": "Simplification of scRNA-seq dataset (old version, not used since 12.02.2021)",
      "topics": [
        "supercell_GE_idx"
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    },
    {
      "page": "supercell_GeneGenePlot",
      "title": "Gene-gene correlation plot",
      "topics": [
        "supercell_GeneGenePlot"
      ]
    },
    {
      "page": "supercell_GeneGenePlot_single",
      "title": "Plot Gene-gene correlation plot for 1 feature",
      "topics": [
        "supercell_GeneGenePlot_single"
      ]
    },
    {
      "page": "supercell_merge",
      "title": "Merging independent SuperCell objects",
      "topics": [
        "supercell_merge"
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    },
    {
      "page": "supercell_mergeGE",
      "title": "Merging metacell gene expression matrices from several independent SuperCell objects",
      "topics": [
        "supercell_mergeGE"
      ]
    },
    {
      "page": "supercell_plot",
      "title": "Plot metacell NW",
      "topics": [
        "supercell_plot"
      ]
    },
    {
      "page": "supercell_plot_GE",
      "title": "Plot super-cell NW colored by an expression of a gene (gradient color)",
      "topics": [
        "supercell_plot_GE"
      ]
    },
    {
      "page": "supercell_plot_tSNE",
      "title": "Plot super-cell tSNE (Use supercell_DimPlot instead) Plots super-cell tSNE (result of supercell_tSNE)",
      "topics": [
        "supercell_plot_tSNE"
      ]
    },
    {
      "page": "supercell_plot_UMAP",
      "title": "Plot super-cell UMAP (Use supercell_DimPlot instead) Plots super-cell UMAP (result of supercell_UMAP)",
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        "supercell_plot_UMAP"
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      "page": "supercell_prcomp",
      "title": "compute PCA for super-cell data (sample-weighted data)",
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      "page": "supercell_rescale",
      "title": "Rescale supercell object",
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      "title": "Compute Silhouette index accounting for samlpe size (super cells size) ###",
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      "title": "Compute UMAP of super-cells",
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      "page": "supercell_VlnPlot",
      "title": "Violin plots",
      "topics": [
        "supercell_VlnPlot"
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    },
    {
      "page": "supercell_VlnPlot_single",
      "title": "Plot Violin plot for 1 feature",
      "topics": [
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      "title": "Combined or independent SuperCell runs for different samples",
      "engine": "knitr::rmarkdown",
      "headings": [
        "A combined analysis -- construction of metacells processing two samples together",
        "Independent analysis -- construction of metacells for each sample independently (applying the same granularity gamma and the same set of features genes.use)",
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      "title": "Example of the SuperCell pipeline",
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        "Analysis",
        "Load scRNA-seq data of 5 cancer cell lines from Tian et al., 2019.",
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