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NAMESPACE
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# Generated by roxygen2: do not edit by hand
S3method(as.CellDataSet,SingleCellExperiment)
S3method(calculate_module_scores,Seurat)
S3method(cluster_cells,SingleCellExperiment)
S3method(cluster_genes,Seurat)
S3method(compute_density,CellDataSet)
S3method(compute_density,SingleCellExperiment)
S3method(compute_density,default)
S3method(compute_jaccard,DataFrame)
S3method(compute_jaccard,SingleCellExperiment)
S3method(compute_jaccard,data.frame)
S3method(compute_percentage_variance,Seurat)
S3method(compute_purity,DataFrame)
S3method(compute_purity,SingleCellExperiment)
S3method(compute_purity,data.frame)
S3method(create_training_sets,Seurat)
S3method(create_training_sets,SingleCellExperiment)
S3method(demux,Seurat)
S3method(expand_column,data.frame)
S3method(filter_cells,SingleCellExperiment)
S3method(filter_cells,matrix)
S3method(filter_genes,SingleCellExperiment)
S3method(filter_genes,matrix)
S3method(fortify,DataFrame)
S3method(get_assay_summary,Seurat)
S3method(get_assay_summary,SingleCellExperiment)
S3method(get_coldata,Seurat)
S3method(get_coldata,SingleCellExperiment)
S3method(get_coldata,seurat)
S3method(get_coord,CellDataSet)
S3method(get_coord,Seurat)
S3method(get_coord,SingleCellExperiment)
S3method(get_coord,seurat)
S3method(get_coord_names,SingleCellExperiment)
S3method(get_coord_names,seurat)
S3method(get_data,Seurat)
S3method(get_rowdata,Seurat)
S3method(get_rowdata,SingleCellExperiment)
S3method(get_rowdata,seurat)
S3method(plot_coord,Seurat)
S3method(plot_coord,SingleCellExperiment)
S3method(plot_coord,data.frame)
S3method(plot_coord,seurat)
S3method(plot_coord2,Seurat)
S3method(plot_gene_modules,Seurat)
S3method(plot_gene_modules_heatmap,Seurat)
S3method(plot_gene_modules_heatmap,matrix)
S3method(plot_heatmap,Seurat)
S3method(plot_heatmap,SingleCellExperiment)
S3method(plot_heatmap,matrix)
S3method(plot_jaccard,DataFrame)
S3method(plot_jaccard,Seurat)
S3method(plot_jaccard,SingleCellExperiment)
S3method(plot_jaccard,data.frame)
S3method(plot_loadings,Seurat)
S3method(plot_pairs,Seurat)
S3method(plot_pseudotime_gene,cell_data_set)
S3method(plot_pseudotime_heatmap,Seurat)
S3method(plot_pseudotime_modules,Seurat)
S3method(plot_purity,DataFrame)
S3method(plot_purity,Seurat)
S3method(plot_purity,SingleCellExperiment)
S3method(plot_purity,data.frame)
S3method(plot_result_rank,data.frame)
S3method(plot_result_rank,haystack)
S3method(plot_spatial,Seurat)
S3method(plot_trajectory,SingleCellExperiment)
S3method(plot_trajectory,SlingshotDataSet)
S3method(plot_trajectory_graph,SingleCellExperiment)
S3method(plot_trajectory_graph,SlingshotDataSet)
S3method(plot_trajectory_graph,layout_ggraph)
S3method(plot_trajectory_graph,tbl_graph)
S3method(plot_violin,Seurat)
S3method(plot_violin,SingleCellExperiment)
S3method(plot_violin,data.frame)
S3method(process,Seurat)
S3method(pseudobulk,Seurat)
S3method(reduce_dim,SingleCellExperiment)
S3method(reduce_dim,matrix)
S3method(run_enrichment,data.frame)
S3method(sample_cells,Seurat)
S3method(sample_cells,SingleCellExperiment)
S3method(sort_features,Seurat)
S3method(sort_features,SingleCellExperiment)
S3method(sort_features,matrix)
export(as.CellDataSet)
export(calculate_cpdb_cellxcell_matrix)
export(calculate_module_scores)
export(cell_density)
export(cluster_cells)
export(cluster_genes)
export(compute_density)
export(compute_jaccard)
export(compute_percentage_variance)
export(compute_purity)
export(create_assay)
export(create_chromatin_assay)
export(create_dimreduc)
export(create_training_sets)
export(demux)
export(demux_cutoff)
export(expand_column)
export(filter_cells)
export(filter_genes)
export(get_assay_summary)
export(get_coldata)
export(get_coord)
export(get_coord_names)
export(get_data)
export(get_expression)
export(get_matrix)
export(get_obsm)
export(get_rowdata)
export(plot_coord)
export(plot_coord2)
export(plot_cpdb_cellxcell)
export(plot_cpdb_cellxpair)
export(plot_cpdb_dotplot)
export(plot_cpdb_heatmap)
export(plot_deg_barplot)
export(plot_enrichment)
export(plot_enrichment_barplot)
export(plot_gene_modules)
export(plot_gene_modules_heatmap)
export(plot_heatmap)
export(plot_jaccard)
export(plot_loadings)
export(plot_pairs)
export(plot_pseudotime_gene)
export(plot_pseudotime_heatmap)
export(plot_pseudotime_modules)
export(plot_purity)
export(plot_result_rank)
export(plot_spatial)
export(plot_trajectory)
export(plot_trajectory_graph)
export(plot_velocity)
export(plot_violin)
export(plot_volcano)
export(process)
export(pseudobulk)
export(read_cpdb_out)
export(reduce_dim)
export(run_enrichment)
export(sample_cells)
export(sort_features)
export(top_deg)
import(Biobase, except = combine)
import(SeuratObject)
import(SingleCellExperiment)
import(SummarizedExperiment, except = Assays)
import(dplyr)
import(ggplot2)
import(tibble)
import(tidyr)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,columnAnnotation)
importFrom(GenomeInfoDb,standardChromosomes)
importFrom(Matrix,t)
importFrom(Seurat,DietSeurat)
importFrom(Seurat,FindClusters)
importFrom(Seurat,FindNeighbors)
importFrom(Seurat,FindVariableFeatures)
importFrom(Seurat,RunPCA)
importFrom(Seurat,RunUMAP)
importFrom(Seurat,ScaleData)
importFrom(forcats,fct_inseq)
importFrom(grid,gpar)
importFrom(grid,grid.circle)
importFrom(grid,unit.c)
importFrom(patchwork,plot_layout)
importFrom(patchwork,wrap_plots)
importFrom(readr,read_tsv)
importFrom(stats,as.dist)
importFrom(stats,cor)
importFrom(stats,cutree)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,kmeans)
importFrom(stats,p.adjust)
importFrom(stats,prcomp)
importFrom(stats,setNames)
importFrom(utils,head)
importFrom(utils,tail)