NAMESPACE

# Generated by roxygen2: do not edit by hand

export(append_colData)
export(benchmark_imputation)
export(bin_granges)
export(bin_scMethrix)
export(binarize)
export(cast_datatable)
export(cast_granges)
export(cluster_scMethrix)
export(colbind)
export(collapse_samples)
export(convert_HDF5_scMethrix)
export(convert_scMethrix)
export(dim_red_scMethrix)
export(export_beds)
export(export_bigwigs)
export(export_bsseq)
export(export_methrix)
export(extract_CpGs)
export(fill)
export(generate_random_subset)
export(generate_training_set)
export(get_distance_matrix)
export(get_matrix)
export(get_metadata_stats)
export(get_region_summary)
export(get_sample_name)
export(get_source_idx)
export(get_stats)
export(has_cov)
export(impute_by_melissa)
export(impute_regions)
export(is_h5)
export(liftover_CpGs)
export(load_HDF5_scMethrix)
export(mask_by_coverage)
export(mask_by_sample)
export(mask_by_variance)
export(mask_helper)
export(merge_scMethrix)
export(parse_source_idx)
export(plot_coverage)
export(plot_density)
export(plot_dim_red)
export(plot_sparsity)
export(plot_stats)
export(plot_violin)
export(prepare_plot_data)
export(read_bed_by_index)
export(read_beds)
export(read_index)
export(reduce_cpgs)
export(remove_assay)
export(remove_uncovered)
export(save_HDF5_scMethrix)
export(scMethrix_theme)
export(split_time)
export(split_vector)
export(start_time)
export(stop_time)
export(subset_ref_cpgs)
export(subset_scMethrix)
export(transform_assay)
exportClasses(scMethrix)
import(DelayedArray)
import(GenomicRanges)
import(HDF5Array)
import(Melissa)
import(Metrics)
import(Rtsne)
import(SingleCellExperiment)
import(SummarizedExperiment)
import(bioDist)
import(data.table, except = c(shift, first, second))
import(doParallel)
import(ggplot2)
import(mclust)
import(parallel)
import(tools)
import(umap)
importClassesFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(BSgenome,getBSgenome)
importFrom(BSgenome,installed.genomes)
importFrom(BSgenome,seqnames)
importFrom(GenomeInfoDb,seqlengths)
importFrom(IRanges,subsetByOverlaps)
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,assays)
importFrom(graphics,axis)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,title)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,setClass)
importFrom(rtracklayer,export)
importFrom(rtracklayer,import.chain)
importFrom(rtracklayer,liftOver)
importFrom(stats,complete.cases)
importFrom(stats,median)
importFrom(stats,prcomp)
importFrom(stats,quantile)
importFrom(stats,sd)
importFrom(stats,var)
importFrom(utils,data)
importFrom(utils,head)
importFrom(utils,menu)
importFrom(utils,write.table)