NAMESPACE

# Generated by roxygen2: do not edit by hand

export(create_rna_atac)
export(enrich_genes)
export(get_associated_prot)
export(get_coverage_plot)
export(get_cts_en_GRNs)
export(get_cts_en_regs)
export(intersect_enhancer_gene_relations)
export(intersect_enhancer_gene_relations_in_batch)
export(intersect_peaks)
export(intersect_peaks_in_batch)
export(plot_dotplot_heatmap)
export(plot_eGRN)
export(plot_stats_genes_and_enhs)
export(prepare_coverage_plot)
export(run_stream)
import(RColorBrewer)
import(Seurat)
import(SingleCellExperiment)
import(SummarizedExperiment)
import(data.table)
import(dplyr)
import(ggplot2)
import(igraph)
import(pbapply)
import(rTRM)
importFrom(BiocGenerics,sort)
importFrom(GenomeInfoDb,seqlevelsStyle)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,resize)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,width)
importFrom(IRanges,IRanges)
importFrom(Matrix,colSums)
importFrom(Matrix,rowSums)
importFrom(Matrix,summary)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(Seurat,DefaultAssay)
importFrom(Seurat,FindClusters)
importFrom(Seurat,FindMultiModalNeighbors)
importFrom(Seurat,RunPCA)
importFrom(Seurat,RunUMAP)
importFrom(Seurat,SCTransform)
importFrom(Signac,Annotation)
importFrom(Signac,FindTopFeatures)
importFrom(Signac,RunSVD)
importFrom(Signac,RunTFIDF)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(igraph,"%--%")
importFrom(igraph,E)
importFrom(igraph,V)
importFrom(igraph,as_ids)
importFrom(igraph,ego)
importFrom(igraph,ends)
importFrom(igraph,neighbors)
importFrom(monocle3,detect_genes)
importFrom(monocle3,estimate_size_factors)
importFrom(monocle3,preprocess_cds)
importFrom(monocle3,reduce_dimension)
importFrom(pbapply,pblapply)
importMethodsFrom(Matrix,t)