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  "Title": "Core Utilities for Single-Cell RNA-Seq",
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  "Description": "Core utilities for single-cell RNA-seq data analysis.\nContained within are utility functions for working with\ndifferential expression (DE) matrices and count matrices, a\ncollection of functions for manipulating and plotting data via\n'ggplot2', and functions to work with cell graphs and cell\nembeddings. Graph-based methods include embedding kNN cell\ngraphs into a UMAP <doi:10.21105/joss.00861>, collapsing\nvertices of each cluster in the graph, and propagating graph\nlabels.",
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  "Author": "Viktor Petukhov [aut], Rasmus Rydbirk [aut], Peter Kharchenko\n[aut], Evan Biederstedt [aut, cre]",
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    "graphToAdjList",
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    "jsDist",
    "mergeCountMatrices",
    "multi2dend",
    "plapply",
    "propagate_labels",
    "propagateLabels",
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    "saveDeAsJson",
    "setMinMax",
    "smooth_count_matrix",
    "smoothChebyshev",
    "smoothSignalOnGraph",
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    "splitVectorByNodes",
    "styleEmbeddingPlot",
    "val2col",
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      "title": "Conos cell annotations",
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      "table": false,
      "tojson": true
    },
    {
      "name": "conosClusterList",
      "title": "Conos clusters list",
      "object": "conosClusterList",
      "class": [
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      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "conosGraph",
      "title": "Conos graph",
      "object": "conosGraph",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
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      "name": "umapEmbedding",
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        "array"
      ],
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      "table": true,
      "tojson": true
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  "_help": [
    {
      "page": "adjacent_vertex_weights",
      "title": "List of adjacent vertex weights from igraph object",
      "topics": [
        "adjacent_vertex_weights"
      ]
    },
    {
      "page": "adjacentVertices",
      "title": "List of adjacent vertices from igraph object",
      "topics": [
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    },
    {
      "page": "appendSpecificityMetricsToDE",
      "title": "Append specificity metrics to DE",
      "topics": [
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    {
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      "topics": [
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      ]
    },
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      "page": "cellAnnotations",
      "title": "Conos cell annotations",
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      "topics": [
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    {
      "page": "collapseCellsByType",
      "title": "Collapse count matrices by cell type, given min/max number of cells",
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      ]
    },
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      "page": "collapseGraphPaga",
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      "topics": [
        "collapseGraphPaga"
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    {
      "page": "collapseGraphSum",
      "title": "Collapse Graph By Sum",
      "topics": [
        "collapseGraphSum"
      ]
    },
    {
      "page": "colSumByFactor",
      "title": "Calculates factor-stratified sums for each column",
      "topics": [
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      ]
    },
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      "page": "conosClusterList",
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    },
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    },
    {
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      "title": "Dot plot adapted from Seurat:::DotPlot, see ?Seurat:::DotPlot for details",
      "topics": [
        "dotPlot"
      ]
    },
    {
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      "title": "Set colors for embedding plot. Used primarily in embeddingPlot().",
      "topics": [
        "embeddingColorsPlot"
      ]
    },
    {
      "page": "embeddingGroupPlot",
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      "topics": [
        "embeddingGroupPlot"
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    },
    {
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      "title": "embeddingPlot generic Plot embedding with provided labels / colors using ggplot2",
      "topics": [
        "embeddingPlot",
        "embeddingPlot,ANY-method",
        "embeddingPlot,Seurat-method",
        "embeddingPlot-methods,ANY",
        "embeddingPlot-methods,Seurat"
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      "topics": [
        "embedGraphUmap"
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    },
    {
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      "topics": [
        "embedKnnGraph"
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      "page": "extendMatrix",
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      "topics": [
        "extendMatrix"
      ]
    },
    {
      "page": "fac2col",
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    {
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      "title": "Get nearest neighbors method on graph",
      "topics": [
        "get_nearest_neighbors"
      ]
    },
    {
      "page": "getClusterGraph",
      "title": "Collapse vertices belonging to each cluster in a graph",
      "topics": [
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    {
      "page": "graphToAdjList",
      "title": "Convert igraph graph into an adjacency list",
      "topics": [
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    },
    {
      "page": "heatFilter",
      "title": "Graph filter with the heat kernel: f(x) = exp(-beta |x / lambda_m - a|^b)",
      "concept": [
        "graph smoothing"
      ],
      "topics": [
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    {
      "page": "jsDist",
      "title": "Jensen–Shannon distance metric (i.e. the square root of the Jensen–Shannon divergence) between the columns of a dense matrix m",
      "topics": [
        "jsDist"
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      "page": "mergeCountMatrices",
      "title": "Merge list of count matrices into a common matrix, entering 0s for the missing entries",
      "topics": [
        "mergeCountMatrices"
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    {
      "page": "multi2dend",
      "title": "Translate multilevel segmentation into a dendrogram, with the lowest level of the dendrogram listing the cells",
      "topics": [
        "multi2dend"
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    },
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      "page": "plapply",
      "title": "Parallel, optionally verbose lapply. See ?parallel::mclapply for more info.",
      "topics": [
        "plapply"
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    },
    {
      "page": "propagate_labels",
      "title": "Label propagation",
      "topics": [
        "propagate_labels"
      ]
    },
    {
      "page": "propagateLabels",
      "title": "Estimate labeling distribution for each vertex, based on provided labels.",
      "topics": [
        "propagateLabels"
      ]
    },
    {
      "page": "propagateLabelsDiffusion",
      "title": "Estimate labeling distribution for each vertex, based on provided labels using a Random Walk on graph",
      "topics": [
        "propagateLabelsDiffusion"
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    },
    {
      "page": "propagateLabelsSolver",
      "title": "Propagate labels using Zhu, Ghahramani, Lafferty (2003) algorithm, \"Semi-Supervised Learning Using Gaussian Fields and Harmonic Functions\" <http://mlg.eng.cam.ac.uk/zoubin/papers/zgl.pdf>",
      "topics": [
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    {
      "page": "saveDeAsJson",
      "title": "Save DE results as JSON tables for viewing in browser",
      "topics": [
        "saveDeAsJson"
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      "page": "setMinMax",
      "title": "Set range for values in object. Changes values outside of range to min or max. Adapted from Seurat::MinMax",
      "topics": [
        "setMinMax"
      ]
    },
    {
      "page": "smooth_count_matrix",
      "title": "Smooth gene expression, used primarily within conos::correctGenes. Used to smooth gene expression values in order to better represent the graph structure. Use diffusion of expression on graph with the equation dv = exp(-a * (v + b))",
      "topics": [
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      "page": "smoothSignalOnGraph",
      "title": "Smooth Signal on Graph",
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      "title": "Set names equal to values, a stats::setNames wrapper function",
      "topics": [
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      "page": "splitVectorByNodes",
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      "topics": [
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    },
    {
      "page": "umapEmbedding",
      "title": "UMAP embedding",
      "topics": [
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      "page": "val2col",
      "title": "Utility function to translate values into colors.",
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      "page": "val2ggcol",
      "title": "Helper function to return a ggplot color gradient for a numeric vector ggplot(aes(color=x, ...), ...) + val2ggcol(x)",
      "topics": [
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