# Generated by roxygen2: do not edit by hand

export(add_chip_peak_labels_to_sites)
export(add_chip_signals_to_sites)
export(assemble_training_data)
export(bin_transform_counts)
export(combine_TOP_samples)
export(count_genome_cuts)
export(count_normalize_chip)
export(extract_TOP_coef_samples)
export(extract_TOP_mean_coef)
export(extract_tf_cell_combos)
export(fimo_motif_matches)
export(fit_TOP_M5_model)
export(get_sites_counts)
export(get_total_reads)
export(index_fa)
export(merge_normalize_bin_transform_counts)
export(merge_normalize_counts)
export(millipede_binning)
export(normalize_bin_transform_counts)
export(normalize_chip)
export(normalize_counts)
export(plot_profile)
export(plot_profile_strands)
export(predict_TOP)
export(process_candidate_sites)
export(scatterplot_predictions)
export(sort_index_idxstats_bam)
import(doParallel)
import(foreach)
import(ggplot2)
importFrom(GenomicRanges,countOverlaps)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(data.table,fread)
importFrom(data.table,fwrite)
importFrom(parallel,detectCores)
