SPONGE/NAMESPACE at master · daisybio/SPONGE · GitHub

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# Generated by roxygen2: do not edit by hand

export(Random_spongEffects)
export(build_classifier_central_genes)
export(calibrate_model)
export(define_modules)
export(enrichment_modules)
export(filter_ceRNA_network)
export(get_central_modules)
export(plot_accuracy_sensitivity_specificity)
export(plot_confusion_matrices)
export(plot_density_scores)
export(plot_heatmaps)
export(plot_involved_miRNAs_to_modules)
export(plot_miRNAs_per_gene)
export(plot_target_gene_expressions)
export(plot_top_modules)
export(prepare_metabric_for_spongEffects)
export(prepare_tcga_for_spongEffects)
export(sample_zero_mscor_cov)
export(sample_zero_mscor_data)
export(sponge)
export(sponge_build_null_model)
export(sponge_compute_p_values)
export(sponge_edge_centralities)
export(sponge_gene_miRNA_interaction_filter)
export(sponge_network)
export(sponge_node_centralities)
export(sponge_plot_network)
export(sponge_plot_network_centralities)
export(sponge_plot_simulation_results)
export(sponge_run_benchmark)
export(sponge_subsampling)
import(Biobase)
import(ComplexHeatmap)
import(MetBrewer)
import(RColorBrewer)
import(biomaRt)
import(caret)
import(cvms)
import(doRNG)
import(dplyr)
import(expm)
import(foreach)
import(ggplot2)
import(ggpubr)
import(ggridges)
import(glmnet)
import(grid)
import(igraph)
import(iterators)
import(logging)
import(miRBaseConverter)
import(pheatmap)
import(randomForest)
import(reshape2)
import(rlang)
import(stringr)
import(tidyr)
import(tidyverse)
import(tnet)
importFrom(Biobase,exprs)
importFrom(MASS,mvrnorm)
importFrom(data.table,as.data.table)
importFrom(data.table,data.table)
importFrom(data.table,rbindlist)
importFrom(data.table,setkey)
importFrom(foreach,foreach)
importFrom(gRbase,combn_prim)
importFrom(gRbase,cov2pcor)
importFrom(glmnet,cv.glmnet)
importFrom(igraph,E)
importFrom(igraph,betweenness)
importFrom(igraph,degree)
importFrom(igraph,edge_betweenness)
importFrom(igraph,eigen_centrality)
importFrom(igraph,graph.data.frame)
importFrom(iterators,icount)
importFrom(iterators,iter)
importFrom(ppcor,pcor)
importFrom(ppcor,pcor.test)
importFrom(stats,coef)
importFrom(stats,cor)
importFrom(stats,cov2cor)
importFrom(stats,df)
importFrom(stats,lm)
importFrom(stats,p.adjust)
importFrom(stats,pf)
importFrom(stats,predict)
importFrom(stats,reorder)
importFrom(stats,rnorm)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,var)
importFrom(stats,xtabs)