NAMESPACE

# Generated by roxygen2: do not edit by hand

export(analyze_tile)
export(atac_call_outliers)
export(atac_normalize_counts)
export(atac_prep_data)
export(atac_timewise_da)
export(atac_training_da)
export(bayesian_graphical_clustering)
export(call_pca_outliers)
export(check_cluster_res_format)
export(cluster_pathway_enrichment)
export(combine_da_results)
export(combine_normalized_data)
export(custom_cluster_pathway_enrichment)
export(df_to_numeric)
export(enrichment_network_vis)
export(extract_main_clusters)
export(extract_tissue_sets)
export(extract_top_trajectories)
export(filter_edge_sets_by_trajectories)
export(filter_outliers)
export(find_flanks)
export(fix_covariates)
export(forest_plot)
export(gene_pathway_enrichment)
export(get_all_trajectories)
export(get_file_from_url)
export(get_peak_annotations)
export(get_rdata_from_url)
export(get_trajectory_sizes_from_edge_sets)
export(get_tree_plot_for_tissue)
export(immuno_timewise_da)
export(immuno_training_da)
export(limit_sets_by_regex)
export(list_available_data)
export(load_atac_feature_annotation)
export(load_epigen_da)
export(load_feature_annotation)
export(load_metab_da)
export(load_methyl_feature_annotation)
export(load_methyl_raw_data)
export(load_sample_data)
export(load_training_da)
export(load_uniprot_human_fasta)
export(make_kegg_db)
export(merge_sites_by_clusters)
export(merge_two_dea_dfs)
export(metab_meta_analysis)
export(metab_meta_regression)
export(metab_timewise_da)
export(metab_training_da)
export(plot_feature_logfc)
export(plot_feature_normalized_data)
export(plot_feature_trajectories)
export(plot_features_per_cluster)
export(plot_pcs)
export(prepare_gsea_input)
export(prepare_ptmsea_input)
export(proteomics_timewise_da)
export(proteomics_training_da)
export(repfdr_wrapper)
export(rrbs_differential_analysis)
export(run_deseq)
export(run_fella)
export(ssGSEA2_wrapper)
export(transcript_call_outliers)
export(transcript_normalize_counts)
export(transcript_prep_data)
export(transcript_timewise_da)
export(transcript_training_da)
export(viallabel_to_pid)
import(MotrpacRatTraining6moData)
importFrom(RColorBrewer,brewer.pal)
importFrom(data.table,":=")
importFrom(data.table,as.data.table)
importFrom(data.table,copy)
importFrom(data.table,data.table)
importFrom(data.table,dcast)
importFrom(data.table,melt)
importFrom(data.table,rbindlist)
importFrom(data.table,setkey)
importFrom(data.table,setnames)
importFrom(dplyr,arrange)
importFrom(dplyr,as_tibble)
importFrom(dplyr,bind_rows)
importFrom(dplyr,case_when)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,if_else)
importFrom(dplyr,mutate)
importFrom(dplyr,relocate)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,summarise_all)
importFrom(dplyr,tibble)
importFrom(dplyr,transmute)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,cpm)
importFrom(edgeR,estimateDisp)
importFrom(edgeR,glmQLFTest)
importFrom(edgeR,glmQLFit)
importFrom(edgeR,topTags)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotate)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_errorbar)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,margin)
importFrom(ggplot2,position_dodge)
importFrom(ggplot2,scale_colour_manual)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_size)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,unit)
importFrom(ggraph,create_layout)
importFrom(ggraph,geom_edge_arc)
importFrom(ggraph,geom_edge_fan0)
importFrom(ggraph,geom_node_point)
importFrom(ggraph,ggraph)
importFrom(ggraph,scale_edge_alpha)
importFrom(ggraph,scale_edge_color_manual)
importFrom(ggraph,scale_edge_colour_identity)
importFrom(ggraph,scale_edge_width)
importFrom(grDevices,boxplot.stats)
importFrom(graphics,hist)
importFrom(graphics,legend)
importFrom(grid,unit)
importFrom(igraph,E)
importFrom(igraph,V)
importFrom(igraph,cluster_louvain)
importFrom(igraph,edge_attr)
importFrom(igraph,graph_from_data_frame)
importFrom(limma,contrasts.fit)
importFrom(limma,eBayes)
importFrom(limma,is.fullrank)
importFrom(limma,lmFit)
importFrom(limma,makeContrasts)
importFrom(limma,topTable)
importFrom(limma,voom)
importFrom(limma,zscoreT)
importFrom(magrittr,"%>%")
importFrom(metap,sumlog)
importFrom(methods,new)
importFrom(purrr,map2_dbl)
importFrom(purrr,map_chr)
importFrom(r2r,hashmap)
importFrom(stats,coefficients)
importFrom(stats,cor)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,phyper)
importFrom(stats,poly)
importFrom(stats,prcomp)
importFrom(stats,sd)
importFrom(tibble,column_to_rownames)
importFrom(tibble,remove_rownames)
importFrom(tidyr,pivot_wider)
importFrom(tidyr,replace_na)
importFrom(tidyr,separate_rows)
importFrom(utils,combn)
importFrom(utils,data)
importFrom(utils,download.file)
importFrom(utils,globalVariables)
importFrom(utils,head)
importFrom(visNetwork,visGroups)
importFrom(visNetwork,visIgraphLayout)
importFrom(visNetwork,visInteraction)
importFrom(visNetwork,visLegend)
importFrom(visNetwork,visNetwork)
importFrom(visNetwork,visSave)