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  "Title": "Single Cell Counts Matrices to PCA",
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  "Description": "> Efficient operations for single cell ATAC-seq fragments\nand RNA counts matrices. Interoperable with standard file\nformats, and introduces efficient bit-packed formats that allow\nlarge storage savings and increased read speeds.",
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    "rotate_x_labels",
    "rowMeans",
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    "set_trackplot_height",
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      "title": "Broadcasting vector arithmetic",
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        "multiply_rows"
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        "all_matrix_inputs<-"
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        "cluster_graph_louvain",
        "cluster_graph_seurat"
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      "topics": [
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    },
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      "topics": [
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        "discrete_palette"
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    },
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      "topics": [
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      "page": "gene_region",
      "title": "Find gene region",
      "topics": [
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      "page": "gene_score_tiles_archr",
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      "topics": [
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        "mouse_gene_mapping"
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    },
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      "topics": [
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        "knn_hnsw"
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    {
      "page": "knn_graph",
      "title": "K Nearest Neighbor (KNN) Graph",
      "topics": [
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        "knn_to_graph",
        "knn_to_snn_graph"
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    },
    {
      "page": "marker_features",
      "title": "Test for marker features",
      "topics": [
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    },
    {
      "page": "gene_matching",
      "title": "Gene symbol matching",
      "topics": [
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        "match_gene_symbol"
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    {
      "page": "matrix_R_conversion",
      "title": "Convert between BPCells matrix and R objects.",
      "topics": [
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    {
      "page": "matrix_stats",
      "title": "Calculate matrix stats",
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      "page": "merge_cells",
      "title": "Merge cells into pseudobulks",
      "topics": [
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      "title": "Merge peaks",
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        "min_by_row",
        "min_scalar"
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      "page": "normalize_ranges",
      "title": "Normalize an object representing genomic ranges",
      "topics": [
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      "page": "nucleosome_counts",
      "title": "Count fragments by nucleosomal size",
      "topics": [
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    },
    {
      "page": "open_fragments_10x",
      "title": "Read/write a 10x fragments file",
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        "write_fragments_10x"
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    },
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      "page": "open_matrix_10x_hdf5",
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      "topics": [
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    {
      "page": "order_ranges",
      "title": "Get end-sorted ordering for genome ranges",
      "topics": [
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    },
    {
      "page": "peak_matrix",
      "title": "Calculate ranges x cells overlap matrix",
      "topics": [
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    },
    {
      "page": "plot_dot",
      "title": "Dotplot",
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      "title": "Plot UMAP or embeddings",
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      "title": "Fragment size distribution",
      "topics": [
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      "page": "plot_read_count_knee",
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      "topics": [
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    },
    {
      "page": "plot_tf_footprint",
      "title": "Plot TF footprint",
      "topics": [
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    },
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      "page": "plot_tss_profile",
      "title": "Plot TSS profile",
      "topics": [
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      "page": "plot_tss_scatter",
      "title": "TSS Enrichment vs. Fragment Counts plot",
      "topics": [
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    },
    {
      "page": "prefix_cell_names",
      "title": "Add sample prefix to cell names",
      "topics": [
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      "page": "qc_scATAC",
      "title": "Calculate ArchR-compatible per-cell QC statistics",
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