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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export("fData<-")
export("pData<-")
export("principal_graph<-")
export("principal_graph_aux<-")
export(aggregate_gene_expression)
export(align_cds)
export(align_transform)
export(choose_cells)
export(choose_graph_segments)
export(clear_cds_slots)
export(cluster_cells)
export(clusters)
export(coefficient_table)
export(combine_cds)
export(compare_models)
export(detect_genes)
export(estimate_size_factors)
export(evaluate_fits)
export(exprs)
export(fData)
export(find_gene_modules)
export(fit_models)
export(fix_missing_cell_labels)
export(generate_garnett_marker_file)
export(get_citations)
export(graph_test)
export(identity_table)
export(learn_graph)
export(load_a549)
export(load_cellranger_data)
export(load_mm_data)
export(load_monocle_objects)
export(load_mtx_data)
export(load_transform_models)
export(load_worm_embryo)
export(load_worm_l2)
export(make_cds_nn_index)
export(make_nn_index)
export(model_predictions)
export(new_cell_data_set)
export(normalized_counts)
export(order_cells)
export(pData)
export(partitions)
export(plot_cells)
export(plot_cells_3d)
export(plot_genes_by_group)
export(plot_genes_in_pseudotime)
export(plot_genes_violin)
export(plot_pc_variance_explained)
export(plot_percent_cells_positive)
export(preprocess_cds)
export(preprocess_transform)
export(principal_graph)
export(principal_graph_aux)
export(pseudotime)
export(reduce_dimension)
export(reduce_dimension_transform)
export(save_monocle_objects)
export(save_transform_models)
export(search_cds_nn_index)
export(search_nn_index)
export(search_nn_matrix)
export(set_cds_nn_index)
export(size_factors)
export(top_markers)
export(transfer_cell_labels)
exportClasses(cell_data_set)
exportMethods("fData<-")
exportMethods("pData<-")
exportMethods("principal_graph<-")
exportMethods("principal_graph_aux<-")
exportMethods(clusters)
exportMethods(exprs)
exportMethods(fData)
exportMethods(pData)
exportMethods(partitions)
exportMethods(principal_graph)
exportMethods(principal_graph_aux)
exportMethods(pseudotime)
import(ggplot2)
importClassesFrom(S4Vectors,List)
importFrom(Biobase,multiassign)
importFrom(Biobase,package.version)
importFrom(BiocGenerics,density)
importFrom(S4Vectors,elementMetadata)
importFrom(S4Vectors,getListElement)
importFrom(SingleCellExperiment,"reducedDim<-")
importFrom(SingleCellExperiment,"reducedDims<-")
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,colData)
importFrom(SingleCellExperiment,counts)
importFrom(SingleCellExperiment,reducedDim)
importFrom(SingleCellExperiment,reducedDims)
importFrom(SingleCellExperiment,rowData)
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,Assays)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,rowRanges)
importFrom(dplyr,"%>%")
importFrom(dplyr,n)
importFrom(future,value)
importFrom(igraph,dfs)
importFrom(lme4,glmer)
importFrom(plyr,".")
importFrom(utils,packageVersion)
useDynLib(monocle3, .registration = TRUE)