NAMESPACE

# Generated by roxygen2: do not edit by hand

export("%>%")
export(allrow_cor)
export(cormat_to_balanced_knn)
export(gen_10x_mars_gene_match)
export(gset_add_genes)
export(gset_get_feat_mat)
export(gset_get_genes)
export(gset_import_table)
export(gset_new_gset)
export(gset_new_restrict_gset)
export(gset_new_restrict_nms)
export(gset_write_table)
export(mc2d_comp_cell_coord)
export(mc2d_comp_graph_coord)
export(mc2d_comp_graph_coord_umap)
export(mc2d_comp_mgraph)
export(mc2d_comp_mgraph_param)
export(mc_colorize)
export(mc_colorize_default)
export(mc_colorize_from_ref_mc)
export(mc_colorize_sup_hierarchy)
export(mc_compute_cov_gc)
export(mc_compute_e_gc)
export(mc_compute_fp)
export(mc_compute_n_bc)
export(mc_compute_outlier_fc)
export(mc_reorder)
export(mc_restrict)
export(mc_set_outlier_mc)
export(mc_update_stats)
export(mcatlas_annotate_mc_by_mc2mc_projection)
export(mcatlas_annotate_mc_by_sc2mc_projection)
export(mcatlas_annotate_mc_by_sc2sc_projection)
export(mcatlas_comp_adj_type_n)
export(mcatlas_project_query)
export(mcell_add_cgraph_bknn_norm_mc)
export(mcell_add_cgraph_from_distmat)
export(mcell_add_cgraph_from_mat_bknn)
export(mcell_add_cgraph_from_mat_raw_knn)
export(mcell_add_gene_stat)
export(mcell_add_mars_facs_data)
export(mcell_batch_stats)
export(mcell_calc_one_batch_stats)
export(mcell_cgraph_norm_gcor)
export(mcell_coclust_filt_by_k_deg)
export(mcell_coclust_from_graph_resamp)
export(mcell_compare_bulk)
export(mcell_gen_atlas)
export(mcell_gen_cell_cor_gset)
export(mcell_gset_add_gene)
export(mcell_gset_filter_cov)
export(mcell_gset_filter_multi)
export(mcell_gset_filter_szcor)
export(mcell_gset_filter_varmean)
export(mcell_gset_from_mc_markers)
export(mcell_gset_remove_clusts)
export(mcell_gset_split_by_dsmat)
export(mcell_import_multi_mars)
export(mcell_import_multi_scmat_10x)
export(mcell_import_scmat_10x)
export(mcell_import_scmat_tsv)
export(mcell_mat_ignore_cells)
export(mcell_mat_ignore_genes)
export(mcell_mat_ignore_small_cells)
export(mcell_mat_rpt_cor_anchors)
export(mcell_mc2d_force_knn)
export(mcell_mc2d_force_knn_on_cells)
export(mcell_mc2d_plot)
export(mcell_mc2d_plot_by_factor)
export(mcell_mc2d_plot_gene)
export(mcell_mc2d_rotate)
export(mcell_mc_add_annot)
export(mcell_mc_add_color)
export(mcell_mc_cell_homogeneity)
export(mcell_mc_coclust_confusion_mat)
export(mcell_mc_confusion_mat)
export(mcell_mc_export_tab)
export(mcell_mc_from_coclust_balanced)
export(mcell_mc_from_coclust_hc)
export(mcell_mc_from_coclust_louv_sub)
export(mcell_mc_hclust_confu)
export(mcell_mc_hierarchy)
export(mcell_mc_match_graph)
export(mcell_mc_plot_by_factor)
export(mcell_mc_plot_confusion)
export(mcell_mc_plot_gg)
export(mcell_mc_plot_hierarchy)
export(mcell_mc_plot_marks)
export(mcell_mc_plot_vgels)
export(mcell_mc_reorder_hc)
export(mcell_mc_screen_outliers_1gene_fold)
export(mcell_mc_split_by_color_group)
export(mcell_mc_split_filt)
export(mcell_mgraph_knn)
export(mcell_mgraph_logistic)
export(mcell_new_mc)
export(mcell_new_mc2d)
export(mcell_new_mc_mgraph)
export(mcell_new_mcatlas)
export(mcell_new_mctnetwork)
export(mcell_pipe_mat2mc2d)
export(mcell_plot_batch_stats)
export(mcell_plot_cross_mc)
export(mcell_plot_gset_cor_mats)
export(mcell_plot_gstats)
export(mcell_plot_outlier_heatmap)
export(mcell_plot_umis_per_cell)
export(mcell_proj_on_atlas)
export(mcell_read_multi_scmat_10x)
export(mcell_read_multi_scmat_mars)
export(mcell_scmat_plot_cmp_kcor)
export(mctnetwork_clust_flows)
export(mctnetwork_comp_manifold_costs)
export(mctnetwork_comp_propagation)
export(mctnetwork_gen_e_gmt_p)
export(mctnetwork_gen_gmod_mc_t)
export(mctnetwork_gen_mincost_flows)
export(mctnetwork_gen_network)
export(mctnetwork_get_flow_mat)
export(mctnetwork_get_type_flows)
export(mctnetwork_propogate_from_t)
export(mgraph_comp_knn)
export(mgraph_comp_logist)
export(rescale_sparse_mat_cols)
export(scdb_add_cgraph)
export(scdb_add_coclust)
export(scdb_add_gene_names_xref)
export(scdb_add_gset)
export(scdb_add_gstat)
export(scdb_add_mat)
export(scdb_add_mc)
export(scdb_add_mc2d)
export(scdb_add_mcatlas)
export(scdb_add_mctnetwork)
export(scdb_add_mgraph)
export(scdb_cgraph)
export(scdb_coclust)
export(scdb_del_cgraph)
export(scdb_del_coclust)
export(scdb_del_gene_names_xref)
export(scdb_del_gset)
export(scdb_del_gstat)
export(scdb_del_mat)
export(scdb_del_mc)
export(scdb_del_mc2d)
export(scdb_del_mcatlas)
export(scdb_del_mctnetwork)
export(scdb_del_mgraph)
export(scdb_gene_names_xref)
export(scdb_gset)
export(scdb_gstat)
export(scdb_init)
export(scdb_is_valid)
export(scdb_ls)
export(scdb_ls_loaded)
export(scdb_mat)
export(scdb_mc)
export(scdb_mc2d)
export(scdb_mcatlas)
export(scdb_mctnetwork)
export(scdb_mgraph)
export(scfigs_dir)
export(scfigs_fn)
export(scfigs_init)
export(scm_downsamp)
export(scm_export_mat_to_sce)
export(scm_gene_stat)
export(scm_ignore_cells)
export(scm_ignore_genes)
export(scm_import_sce_to_mat)
export(scm_merge_mats)
export(scm_new_matrix)
export(scm_sub_mat)
export(scm_which_downsamp_n)
export(scmat_read_scmat_10x)
export(scmat_read_scmat_10x_custom)
export(tgCellGraph)
export(tgCoClust)
export(tgGeneSets)
export(tgMC2D)
export(tgMCAtlas)
export(tgMCCov)
export(tgMCManifGraph)
export(tgMCTNetwork)
export(tgScMat)
exportClasses(tgCellGraph)
exportClasses(tgCoClust)
exportClasses(tgGeneSets)
exportClasses(tgMC2D)
exportClasses(tgMCAtlas)
exportClasses(tgMCCov)
exportClasses(tgMCManifGraph)
exportClasses(tgMCTNetwork)
exportClasses(tgScMat)
exportMethods(initialize)
import(Matrix)
import(dplyr)
import(ggplot2)
import(methods)
import(tgconfig)
import(tgstat)
import(tgutil)
importClassesFrom(Matrix,Matrix)
importClassesFrom(Matrix,dgCMatrix)
importClassesFrom(Matrix,dgeMatrix)
importClassesFrom(graph,graphNEL)
importFrom(Rgraphviz,layoutGraph)
importFrom(cluster,silhouette)
importFrom(dbscan,dbscan)
importFrom(graph,addEdge)
importFrom(graph,addNode)
importFrom(graph,nodeRenderInfo)
importFrom(graph,plot)
importFrom(igraph,cluster_louvain)
importFrom(igraph,graph_from_data_frame)
importFrom(magrittr,"%>%")
importFrom(parallel,mclapply)
importFrom(pdist,pdist)
importFrom(tidyr,gather)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,pivot_wider)
importFrom(tidyr,spread)
importFrom(umap,umap)
importFrom(zoo,rollmean)
importFrom(zoo,rollmedian)