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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
S3method(DefaultNetwork,GRNData)
S3method(DefaultNetwork,RegulatoryNetwork)
S3method(GetAssay,GRNData)
S3method(GetAssaySummary,GRNData)
S3method(GetAssaySummary,Seurat)
S3method(GetGRN,GRNData)
S3method(GetNetwork,GRNData)
S3method(GetNetwork,RegulatoryNetwork)
S3method(LayerData,GRNData)
S3method(NetworkFeatures,GRNData)
S3method(NetworkFeatures,RegulatoryNetwork)
S3method(NetworkGraph,GRNData)
S3method(NetworkGraph,Network)
S3method(NetworkGraph,RegulatoryNetwork)
S3method(NetworkModules,GRNData)
S3method(NetworkModules,Network)
S3method(NetworkModules,RegulatoryNetwork)
S3method(NetworkParams,GRNData)
S3method(NetworkParams,Network)
S3method(NetworkParams,RegulatoryNetwork)
S3method(NetworkRegions,GRNData)
S3method(NetworkRegions,RegulatoryNetwork)
S3method(NetworkTFs,GRNData)
S3method(NetworkTFs,RegulatoryNetwork)
S3method(Params,GRNData)
S3method(Params,RegulatoryNetwork)
S3method(VariableFeatures,GRNData)
S3method(coef,GRNData)
S3method(coef,Network)
S3method(coef,RegulatoryNetwork)
S3method(find_modules,GRNData)
S3method(find_modules,Network)
S3method(find_motifs,GRNData)
S3method(get_network_graph,GRNData)
S3method(get_tf_network,GRNData)
S3method(gof,GRNData)
S3method(gof,Network)
S3method(gof,RegulatoryNetwork)
S3method(infer_grn,GRNData)
S3method(initiate_grn,GRNData)
S3method(initiate_grn,Seurat)
S3method(plot_gof,GRNData)
S3method(plot_module_metrics,GRNData)
S3method(plot_network_graph,GRNData)
S3method(plot_tf_network,GRNData)
S3method(print,Modules)
S3method(print,Network)
S3method(print,Regions)
S3method(print,RegulatoryNetwork)
export(DefaultNetwork)
export(GetAssay)
export(GetAssaySummary)
export(GetGRN)
export(GetNetwork)
export(LayerData)
export(NetworkFeatures)
export(NetworkGraph)
export(NetworkModules)
export(NetworkParams)
export(NetworkRegions)
export(NetworkTFs)
export(Params)
export(VariableFeatures)
export(aggregate_assay)
export(aggregate_matrix)
export(create_GRNData)
export(find_modules)
export(find_motifs)
export(find_peaks_near_genes)
export(fit_bagging_ridge)
export(fit_bayesian_ridge)
export(fit_brms)
export(fit_cvglmnet)
export(fit_glm)
export(fit_glmnet)
export(fit_grn_models)
export(fit_model)
export(fit_xgb)
export(format_coefs)
export(get_network_graph)
export(get_tf_network)
export(gof)
export(infer_grn)
export(initiate_grn)
export(map_par)
export(no_legend)
export(no_margin)
export(no_x_text)
export(no_y_text)
export(plot_gof)
export(plot_module_metrics)
export(plot_network_graph)
export(plot_tf_network)
export(sparse_cor)
exportClasses(GRNData)
exportClasses(Network)
exportClasses(Regions)
exportClasses(RegulatoryNetwork)
import(Matrix)
import(dplyr)
import(ggplot2)
import(ggpointdensity)
import(ggraph)
import(pals)
import(patchwork)
import(sparseMatrixStats)
import(stringr)
import(tibble)
import(tidygraph)
importClassesFrom(GenomicRanges,GRanges)
importClassesFrom(SeuratObject,Seurat)
importClassesFrom(Signac,Motif)
importFrom(IRanges,findOverlaps)
importFrom(IRanges,pintersect)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(Seurat,GetAssay)
importFrom(Seurat,VariableFeatures)
importFrom(Signac,StringToGRanges)
importFrom(dplyr,distinct)
importFrom(dplyr,mutate)
importFrom(dplyr,select)
importFrom(methods,setClass)
importFrom(purrr,map)
importFrom(purrr,map_chr)
importFrom(purrr,map_dbl)
importFrom(purrr,map_dfr)
importFrom(purrr,map_lgl)
importFrom(stringr,str_replace_all)
importFrom(stringr,str_split)
importFrom(tidyr,pivot_longer)