platt/NAMESPACE at main · cole-trapnell-lab/platt · GitHub

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# Generated by roxygen2: do not edit by hand

export(assemble_mt_graph)
export(assemble_partition)
export(assemble_timeseries_transitions)
export(assemble_transition_graph_from_perturbations)
export(assemble_wt_graph)
export(assess_perturbation_effects)
export(assess_support_for_transition_graph)
export(break_cycles_in_state_transition_graph)
export(calc_graph_overrep_genes)
export(calc_gsea_enrichment_on_state_specific_genes)
export(calc_overrep_genes)
export(calc_pathway_enrichment_on_state_specific_genes)
export(calculate_dvegs)
export(categorize_genetic_requirements)
export(collect_coefficients_for_shrinkage)
export(collect_genotype_effects)
export(compare_gene_expression_within_node)
export(compare_genes_in_cell_state)
export(compare_genes_over_graph)
export(compare_genes_within_state_graph)
export(contract_state_graph)
export(estimate_ambient_rna)
export(find_cycles)
export(fit_genotype_ccm)
export(fit_genotype_deg)
export(fit_mt_models)
export(fit_subset_genotype_ccm)
export(fit_wt_model)
export(get_discordant_loss_pairs)
export(get_extant_cell_types)
export(get_graph_layout)
export(get_perturbation_effects)
export(get_perturbation_paths)
export(get_time_window)
export(init_pathfinding_graph)
export(layout_state_graph)
export(make_contrast)
export(new_cell_state_graph)
export(plot_abundance_changes)
export(plot_annotations)
export(plot_by_support)
export(plot_by_table)
export(plot_cell_type_control_kinetics)
export(plot_cell_type_perturb_kinetics)
export(plot_degs)
export(plot_gene_expr)
export(subcluster_cds)
exportClasses(cell_state_graph)
import(Matrix)
import(Rgraphviz)
import(assertthat)
import(dplyr)
import(fgsea)
import(ggforce)
import(ggnetwork)
import(ggnewscale)
import(ggplot2)
import(ggrepel)
import(igraph)
import(mgcv)
import(purrr)
import(speedglm)
import(stringr)
import(tibble)
import(tidyr)
import(viridis)
importFrom(Matrix,colSums)
importFrom(Matrix,rowSums)
importFrom(Matrix,t)
importFrom(ashr,ash)
importFrom(assertthat,assert_that)
importFrom(dplyr,"%>%")
importFrom(dplyr,case_when)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,pull)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,slice_max)
importFrom(dplyr,slice_min)
importFrom(dplyr,summarize)
importFrom(dplyr,top_n)
importFrom(ggplot2,aes)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_y_log10)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(graph,graphAM)
importFrom(graph,subGraph)
importFrom(grid,unit)
importFrom(igraph,V)
importFrom(igraph,as_data_frame)
importFrom(igraph,graph_from_data_frame)
importFrom(magrittr,"%>%")
importFrom(matrixStats,rowMaxs)
importFrom(monocle3,aggregate_gene_expression)
importFrom(pheatmap,pheatmap)
importFrom(purrr,map)
importFrom(purrr,map2)
importFrom(purrr,map_int)
importFrom(purrr,possibly)
importFrom(rlang,sym)
importFrom(stats,ave)
importFrom(stats,p.adjust)
importFrom(stats,pnorm)
importFrom(stats,predict)
importFrom(stats,setNames)
importFrom(stringr,str_replace_all)
importFrom(stringr,str_split)
importFrom(stringr,str_split_fixed)
importFrom(tibble,column_to_rownames)
importFrom(tibble,rownames_to_column)
importFrom(tibble,tibble)
importFrom(tidyr,nest)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,pivot_wider)
importFrom(tidyr,tibble)
importFrom(tidyr,unnest)
importFrom(utils,head)
importFrom(utils,tail)
importFrom(utils,write.csv)
importFrom(viridis,viridis)