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      "page": "Ape.setFeatures",
      "title": "Set the FEATURES Slot of a GRanges Object",
      "topics": [
        "Ape.setFeatures"
      ]
    },
    {
      "page": "as.cell_data_set",
      "title": "Convert objects to Monocle3 'cell_data_set' objects",
      "topics": [
        "as.CellDataSet",
        "as.cell_data_set",
        "as.cell_data_set.Seurat"
      ]
    },
    {
      "page": "as.Seurat.extras",
      "title": "Convert single cell experiment to Seurat",
      "topics": [
        "as.Seurat.cell_data_set"
      ]
    },
    {
      "page": "bb_aggregate",
      "title": "Aggregate Single Cell Gene Expression",
      "topics": [
        "bb_aggregate"
      ]
    },
    {
      "page": "bb_align",
      "title": "Align a CDS object according to a metadata variable",
      "topics": [
        "bb_align"
      ]
    },
    {
      "page": "bb_annotate_npc",
      "title": "Annotate a Plot using NPC Coordinates",
      "topics": [
        "bb_annotate_npc"
      ]
    },
    {
      "page": "bb_blind_images",
      "title": "Make a Copy of Image Files and Rename With File Hashes in Blinded Folder",
      "topics": [
        "bb_blind_images"
      ]
    },
    {
      "page": "bb_buff_granges",
      "title": "Clean Up Your GRanges Object",
      "topics": [
        "bb_buff_granges"
      ]
    },
    {
      "page": "bb_cds_anno",
      "title": "Annotate a CDS by Label Transfer",
      "topics": [
        "bb_cds_anno"
      ]
    },
    {
      "page": "bb_cds_heatmap",
      "title": "Make a Heatmap of Aggregated Gene Expressionf from a CDS",
      "topics": [
        "bb_cds_heatmap"
      ]
    },
    {
      "page": "bb_cellchat",
      "title": "Infer Cell-Cell Communication",
      "topics": [
        "bb_cellchat"
      ]
    },
    {
      "page": "bb_cellchat_heatmap",
      "title": "Make a Complex Heatmap From a CellChat Object With Sensible Defaults",
      "topics": [
        "bb_cellchat_heatmap"
      ]
    },
    {
      "page": "bb_cellmeta",
      "title": "Get Cell Metadata",
      "topics": [
        "bb_cellmeta"
      ]
    },
    {
      "page": "bb_cite_umap",
      "title": "Plot a UMAP Showing Cite-Seq Antibody Binding",
      "topics": [
        "bb_cite_umap"
      ]
    },
    {
      "page": "bb_cluster_representation",
      "title": "Cluster Representation By Fisher Exact Test Per Cell",
      "topics": [
        "bb_cluster_representation"
      ]
    },
    {
      "page": "bb_cluster_representation2",
      "title": "Cluster Representation By Regression Per Sample",
      "topics": [
        "bb_cluster_representation2"
      ]
    },
    {
      "page": "bb_daseq",
      "title": "Calculate Differential Abundance Using DAseq",
      "topics": [
        "bb_daseq"
      ]
    },
    {
      "page": "bb_doubletfinder",
      "title": "Use doubletfinder to model and mark doublets",
      "topics": [
        "bb_doubletfinder"
      ]
    },
    {
      "page": "bb_extract_msig",
      "title": "Extract MSIGDB Gene Sets",
      "topics": [
        "bb_extract_msig"
      ]
    },
    {
      "page": "bb_fix_file_path",
      "title": "Convert windows filepath to linux-compatible.",
      "topics": [
        "bb_fix_file_path"
      ]
    },
    {
      "page": "bb_fragment_replacement",
      "title": "Replace The Path to a Fragment File In a Signac Object",
      "topics": [
        "bb_fragment_replacement"
      ]
    },
    {
      "page": "bb_gene_dotplot",
      "title": "Make a dotplot of gene expression by cell population",
      "topics": [
        "bb_gene_dotplot"
      ]
    },
    {
      "page": "bb_gene_modules",
      "title": "A function to generate gene modules and add them to the Gene Metadata",
      "topics": [
        "bb_gene_modules"
      ]
    },
    {
      "page": "bb_gene_pseudotime",
      "title": "Plot expression of a gene or genes in pseudotime.",
      "topics": [
        "bb_gene_pseudotime"
      ]
    },
    {
      "page": "bb_gene_umap",
      "title": "Make a Plot of Gene Expression in UMAP Form",
      "topics": [
        "bb_gene_umap"
      ]
    },
    {
      "page": "bb_gene_violinplot",
      "title": "Make a plot of gene expression in UMAP form",
      "topics": [
        "bb_gene_violinplot"
      ]
    },
    {
      "page": "bb_genebubbles",
      "title": "Create a Gene Bubble/Dot Plot",
      "topics": [
        "bb_genebubbles"
      ]
    },
    {
      "page": "bb_goenrichment",
      "title": "Go Term Enrichment",
      "topics": [
        "bb_goenrichment"
      ]
    },
    {
      "page": "bb_goscatter",
      "title": "Make a scatter plot of GO term associations",
      "topics": [
        "bb_goscatter"
      ]
    },
    {
      "page": "bb_gosummary",
      "title": "A function to reduce go terms by semantic similarity",
      "topics": [
        "bb_gosummary"
      ]
    },
    {
      "page": "bb_import_bw",
      "title": "Import a Big Wig File",
      "topics": [
        "bb_import_bw"
      ]
    },
    {
      "page": "bb_import_seacr_peaks",
      "title": "Import Peaks from SEACR",
      "topics": [
        "bb_import_macs_narrowpeaks",
        "bb_import_seacr_peaks"
      ]
    },
    {
      "page": "bb_load_tenx_h5",
      "title": "Load a 10X Genomics H5 File and Return a CDS",
      "topics": [
        "bb_load_tenx_h5"
      ]
    },
    {
      "page": "bb_loupeR",
      "title": "Create a Loupe File from a Cell Data Set",
      "topics": [
        "bb_loupeR"
      ]
    },
    {
      "page": "bb_make_ape_genomic",
      "title": "Make an Ape Genome Object",
      "topics": [
        "bb_make_ape_genomic"
      ]
    },
    {
      "page": "bb_make_ape_transcript",
      "title": "Make an Ape Transcriptome Object",
      "topics": [
        "bb_make_ape_transcript"
      ]
    },
    {
      "page": "bb_makeTrace",
      "title": "Construct a Trace object from a Signac Object or Granges object",
      "topics": [
        "bb_makeTrace"
      ]
    },
    {
      "page": "bb_merge_narrowpeaks",
      "title": "A Function To Merge Replicate Narrow Peaks GRanges",
      "topics": [
        "bb_merge_narrowpeaks"
      ]
    },
    {
      "page": "bb_metafeature",
      "title": "A Function to Generate Data For Making MetaPlots",
      "topics": [
        "bb_metafeature"
      ]
    },
    {
      "page": "bb_monocle_",
      "title": "Annotate Single cell Data Using Monocle3",
      "topics": [
        "bb_monocle_",
        "bb_monocle_anno",
        "bb_monocle_project"
      ]
    },
    {
      "page": "bb_monocle_regression",
      "title": "A function to perform regression on single cell data.",
      "topics": [
        "bb_monocle_regression"
      ]
    },
    {
      "page": "bb_monocle_regression_better",
      "title": "An Improved Function to Perform Regression on Single Cell Data.",
      "topics": [
        "bb_monocle_regression_better"
      ]
    },
    {
      "page": "bb_parseape",
      "title": "Parse a Genebank File and Construct an APE Object",
      "topics": [
        "bb_parseape"
      ]
    },
    {
      "page": "bb_plot_genes_in_pseudotime",
      "title": "Plots expression for one or more genes as a function of pseudotime",
      "topics": [
        "bb_plot_genes_in_pseudotime"
      ]
    },
    {
      "page": "bb_plot_heatmap_colData",
      "title": "Plot SummarizedHeatmap colData",
      "topics": [
        "bb_plot_heatmap_colData"
      ]
    },
    {
      "page": "bb_plot_heatmap_colDendro",
      "title": "Plot a Heatmap Column Dendrogram",
      "topics": [
        "bb_plot_heatmap_colDendro"
      ]
    },
    {
      "page": "bb_plot_heatmap_colHighlight",
      "title": "Plot a Column Highlight",
      "topics": [
        "bb_plot_heatmap_colHighlight"
      ]
    },
    {
      "page": "bb_plot_heatmap_main",
      "title": "Plot the Body of Heatmap",
      "topics": [
        "bb_plot_heatmap_main"
      ]
    },
    {
      "page": "bb_plot_heatmap_rowData",
      "title": "Plot a SummarizedHeatmap rowData",
      "topics": [
        "bb_plot_heatmap_rowData"
      ]
    },
    {
      "page": "bb_plot_heatmap_rowDendro",
      "title": "Plot a Heatmap Row Dendrogram",
      "topics": [
        "bb_plot_heatmap_rowDendro"
      ]
    },
    {
      "page": "bb_plot_heatmap_rowHighlight",
      "title": "Plot a Row Highlight",
      "topics": [
        "bb_plot_heatmap_rowHighlight"
      ]
    },
    {
      "page": "bb_plot_rowData_col",
      "title": "A helper function to generate a data frame in the proper form for aggregate expression plotting with bb_gene_umap.",
      "topics": [
        "bb_plot_rowData_col"
      ]
    },
    {
      "page": "bb_plot_trace_axis",
      "title": "Plot The X Axis From A Trace Object",
      "topics": [
        "bb_plot_trace_axis"
      ]
    },
    {
      "page": "bb_plot_trace_data",
      "title": "Plot The Trace Data From A Trace Object",
      "topics": [
        "bb_plot_trace_data"
      ]
    },
    {
      "page": "bb_plot_trace_links",
      "title": "Plot The Link Data From A Trace Object",
      "topics": [
        "bb_plot_trace_links"
      ]
    },
    {
      "page": "bb_plot_trace_model",
      "title": "Plot The Gene Model From A Trace Object",
      "topics": [
        "bb_plot_trace_model"
      ]
    },
    {
      "page": "bb_plot_trace_peaks",
      "title": "Plot The peak Data From A Trace Object",
      "topics": [
        "bb_plot_trace_peaks"
      ]
    },
    {
      "page": "bb_plotfootprint",
      "title": "Plot motif footprinting results",
      "concept": [
        "footprinting",
        "visualization"
      ],
      "topics": [
        "bb_plotfootprint"
      ]
    },
    {
      "page": "bb_print_full_stats",
      "title": "Print out a stats report",
      "topics": [
        "bb_print_full_stats"
      ]
    },
    {
      "page": "bb_promoter_overlap",
      "title": "Calculate The Overlap Between Peaks and Promoters",
      "topics": [
        "bb_promoter_overlap"
      ]
    },
    {
      "page": "bb_pseudobulk_mf",
      "title": "Run Multifactor Pseudobulk Analysis using Deseq2",
      "topics": [
        "bb_pseudobulk_mf"
      ]
    },
    {
      "page": "bb_pseudocells",
      "title": "Generate a CDS from Bulk RNA-seq data",
      "topics": [
        "bb_pseudocells"
      ]
    },
    {
      "page": "bb_pseudotime",
      "title": "Learn Graph and Calculate Pseudotime",
      "topics": [
        "bb_pseudotime"
      ]
    },
    {
      "page": "bb_qc",
      "title": "A function to run qc tests on cds objects.",
      "topics": [
        "bb_qc"
      ]
    },
    {
      "page": "bb_read_bam",
      "title": "Read Bam Files",
      "topics": [
        "bb_read_bam"
      ]
    },
    {
      "page": "bb_read_narrowpeak",
      "title": "A Function to Read In Narrow Peaks Files",
      "topics": [
        "bb_read_narrowpeak"
      ]
    },
    {
      "page": "bb_rejoin",
      "title": "Rejoin qc and doubletfinder data to a cds object",
      "topics": [
        "bb_rejoin"
      ]
    },
    {
      "page": "bb_remove_dupes",
      "title": "Remove rows that have duplicates in a given column",
      "topics": [
        "bb_remove_dupes"
      ]
    },
    {
      "page": "bb_rowmeta",
      "title": "Get Feature/Gene Metadata",
      "topics": [
        "bb_rowmeta"
      ]
    },
    {
      "page": "bb_seurat_anno",
      "title": "A function to generate automated cell labelings with Seurat",
      "topics": [
        "bb_seurat_anno"
      ]
    },
    {
      "page": "bb_souporcell_matrix",
      "title": "Build a Souporcell genotype-by-SNP allele-fraction matrix",
      "topics": [
        "bb_souporcell_matrix"
      ]
    },
    {
      "page": "bb_split_atac",
      "title": "Split Out Peaks Data",
      "topics": [
        "bb_split_atac"
      ]
    },
    {
      "page": "bb_split_citeseq",
      "title": "Split Antibody Capture Data into Alt Experiment",
      "topics": [
        "bb_split_citeseq"
      ]
    },
    {
      "page": "bb_tbl_to_coldata",
      "title": "A Function To Add Tibble Columns To Cell Metadata",
      "topics": [
        "bb_tbl_to_coldata"
      ]
    },
    {
      "page": "bb_tbl_to_matrix",
      "title": "Convert a wide-form tibble a matrix",
      "topics": [
        "bb_tbl_to_matrix"
      ]
    },
    {
      "page": "bb_tbl_to_rowdata",
      "title": "A Function To Add Tibble Columns To Feature Metadata",
      "topics": [
        "bb_tbl_to_rowdata"
      ]
    },
    {
      "page": "bb_triplecluster",
      "title": "A function to generate clusters from scRNA-seq data",
      "topics": [
        "bb_triplecluster"
      ]
    },
    {
      "page": "bb_unblind_images",
      "title": "Rejoin Blinded Scores to Original File Names",
      "topics": [
        "bb_unblind_images"
      ]
    },
    {
      "page": "bb_var_umap",
      "title": "A function to generate a UMAP with colors mapped to colData variables",
      "topics": [
        "bb_var_umap"
      ]
    },
    {
      "page": "COMMENTS",
      "title": "Get the Comments Slot from an Ape Object",
      "topics": [
        "COMMENTS"
      ]
    },
    {
      "page": "data_median_se",
      "title": "Generate median +/- se stat object for jitter ggplot",
      "topics": [
        "data_median_se"
      ]
    },
    {
      "page": "data_summary_mean_sd",
      "title": "Generate mean +/- sd stat object for jitter ggplot",
      "topics": [
        "data_summary_mean_sd"
      ]
    },
    {
      "page": "data_summary_mean_se",
      "title": "Generate mean +/- se stat object for jitter ggplot",
      "topics": [
        "data_summary_mean_se"
      ]
    },
    {
      "page": "data_summary_median_iqr",
      "title": "Generate median +/- iqr stat object for jitter ggplot",
      "topics": [
        "data_summary_median_iqr"
      ]
    },
    {
      "page": "data_summary_median_mad",
      "title": "Generate median +/- mad stat object for jitter ggplot",
      "topics": [
        "data_summary_median_mad"
      ]
    },
    {
      "page": "dMcast",
      "title": "Casts or pivots a long 'data frame' into a wide sparse matrix",
      "topics": [
        "dMcast"
      ]
    },
    {
      "page": "FEATURES",
      "title": "Get the Features Slot from an Ape Object",
      "topics": [
        "FEATURES"
      ]
    },
    {
      "page": "filter_cds",
      "title": "Filter a CDS",
      "topics": [
        "filter_cds"
      ]
    },
    {
      "page": "geom_sig_annotations",
      "title": "Build significance annotation geoms",
      "topics": [
        "geom_sig_annotations"
      ]
    },
    {
      "page": "geom_sig_table",
      "title": "Significance-table annotations for ggplot2 discrete x-axes",
      "topics": [
        "geom_sig_table"
      ]
    },
    {
      "page": "geom_split_violin",
      "title": "geom_split_violin",
      "topics": [
        "geom_split_violin"
      ]
    },
    {
      "page": "granges_to_features",
      "title": "Format a GRanges Object as a Character Vector For Inclusion in Genebank File",
      "topics": [
        "granges_to_features"
      ]
    },
    {
      "page": "Image-class",
      "title": "An S4 Class for Holding Image Metadata",
      "topics": [
        "file_path",
        "file_path<-",
        "filter",
        "filter<-",
        "genetics",
        "genetics<-",
        "Image",
        "Image-class",
        "Image_",
        "Image_-class",
        "mag",
        "mag<-",
        "microscope",
        "microscope<-",
        "note",
        "note<-",
        "show,Image_-method",
        "species",
        "species<-",
        "stage",
        "stage<-",
        "treatment",
        "treatment<-",
        "use",
        "use<-"
      ]
    },
    {
      "page": "ImageCatalog-class",
      "title": "An S4 Image Catalog",
      "topics": [
        "$,ImageCatalog-method",
        "ImageCatalog",
        "ImageCatalog-class",
        "ImageCatalog.add",
        "ImageCatalog.as_tibble",
        "ImageCatalog.delete",
        "ImageCatalog.write",
        "show,ImageCatalog-method",
        "[,ImageCatalog,ANY,ANY,ANY-method",
        "[[,ImageCatalog,ANY,ANY-method"
      ]
    },
    {
      "page": "LearnGraph",
      "title": "Run 'link[monocle3]{learn_graph}' on a 'Seurat' object",
      "topics": [
        "LearnGraph"
      ]
    },
    {
      "page": "LOCUS",
      "title": "Get the Locus Slot from an Ape Object",
      "topics": [
        "LOCUS"
      ]
    },
    {
      "page": "merge.Matrix",
      "title": "Merges two Matrices or matrix-like objects",
      "topics": [
        "join.Matrix",
        "merge.Matrix"
      ]
    },
    {
      "page": "normalize_batch",
      "title": "Noramalize a Data Table by Group and Batch",
      "topics": [
        "normalize_batch"
      ]
    },
    {
      "page": "prepare_sig_annotations",
      "title": "Prepare significance annotation data for a ggplot",
      "topics": [
        "prepare_sig_annotations"
      ]
    },
    {
      "page": "project_data",
      "title": "Activate Project Data",
      "topics": [
        "project_data"
      ]
    },
    {
      "page": "rBind.fill",
      "title": "Combine matrixes by row, fill in missing columns",
      "topics": [
        "rBind.fill"
      ]
    },
    {
      "page": "save_monocle_disk",
      "title": "Save a monocle3 cds object on disk",
      "topics": [
        "save_monocle_disk"
      ]
    },
    {
      "page": "se",
      "title": "Calculate standard error of the mean",
      "topics": [
        "se"
      ]
    },
    {
      "page": "show-Ape-method",
      "title": "Show an Ape Object",
      "topics": [
        "show,Ape-method"
      ]
    },
    {
      "page": "show-Trace-method",
      "title": "Show a Trace Object",
      "topics": [
        "show,Trace-method"
      ]
    },
    {
      "page": "SummarizedHeatmap",
      "title": "An S4 Class for Holding Heatmap Data",
      "topics": [
        ".SummarizedHeatmap",
        "SummarizedHeatmap",
        "SummarizedHeatmap-class"
      ]
    },
    {
      "page": "Trace-class",
      "title": "An S4 class to Hold Genome Track Data",
      "topics": [
        "Trace",
        "Trace-class"
      ]
    },
    {
      "page": "Trace.data",
      "title": "Get the Trace Data Slot from a Trace Object",
      "topics": [
        "Trace.data"
      ]
    },
    {
      "page": "Trace.gene_model",
      "title": "Get the gene_model Slot from a Trace Object",
      "topics": [
        "Trace.gene_model"
      ]
    },
    {
      "page": "Trace.links",
      "title": "Get the Links Slot from a Trace Object",
      "topics": [
        "Trace.links"
      ]
    },
    {
      "page": "Trace.peaks",
      "title": "Get the peaks Slot from a Trace Object",
      "topics": [
        "Trace.peaks"
      ]
    },
    {
      "page": "Trace.plot_range",
      "title": "Get the plot_range Slot from a Trace Object",
      "topics": [
        "Trace.plot_range"
      ]
    },
    {
      "page": "Trace.setData",
      "title": "Set the Trace Data Slot of a GRanges Object",
      "topics": [
        "Trace.setData"
      ]
    },
    {
      "page": "Trace.setLinks",
      "title": "Set the Links Slot of a GRanges Object",
      "topics": [
        "Trace.setLinks"
      ]
    },
    {
      "page": "Trace.setpeaks",
      "title": "Set the peaks Slot of a GRanges Object",
      "topics": [
        "Trace.setpeaks"
      ]
    },
    {
      "page": "Trace.setRange",
      "title": "Set the Plot Range Slot of a GRanges Object",
      "topics": [
        "Trace.setRange"
      ]
    }
  ],
  "_readme": "https://github.com/blaserlab/blaseRtools/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "annotate",
    "AnnotationDbi",
    "ashr",
    "askpass",
    "assertthat",
    "assorthead",
    "backports",
    "base64enc",
    "batchelor",
    "beachmat",
    "beeswarm",
    "BH",
    "biglm",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocIO",
    "biocmake",
    "BiocManager",
    "BiocNeighbors",
    "BiocParallel",
    "BiocSingular",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blaseRdata",
    "blaseRtemplates",
    "blob",
    "boot",
    "BPCells",
    "brew",
    "brio",
    "broom",
    "BSgenome",
    "BSgenome.Drerio.UCSC.danRer11",
    "BSgenome.Hsapiens.UCSC.hg38",
    "bslib",
    "cachem",
    "Cairo",
    "callr",
    "car",
    "carData",
    "caret",
    "caTools",
    "CellChat",
    "cellranger",
    "cigarillo",
    "circlize",
    "class",
    "classInt",
    "cli",
    "clipr",
    "clock",
    "clue",
    "cluster",
    "coda",
    "codetools",
    "collapse",
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