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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
S3method("[",anchors)
S3method(`expnames<-`,ARMLA_discovery)
S3method(`expnames<-`,RCP_discovery)
S3method(`expnames<-`,chrommat_discovery)
S3method(`expnames<-`,contacts)
S3method(`expnames<-`,default)
S3method(`expnames<-`,genomescore_discovery)
S3method(`expnames<-`,saddle_discovery)
S3method(as.double,contacts)
S3method(as.double,discovery)
S3method(as.matrix,contacts_matrix)
S3method(as_track,CS_discovery)
S3method(as_track,DI_discovery)
S3method(as_track,IS_discovery)
S3method(as_track,LayerInstance)
S3method(as_track,domainogram_discovery)
S3method(as_track,virtual4C_discovery)
S3method(bundle,ARMLA_discovery)
S3method(bundle,CS_discovery)
S3method(bundle,DI_discovery)
S3method(bundle,IIT_discovery)
S3method(bundle,IS_discovery)
S3method(bundle,RCP_discovery)
S3method(bundle,chrommat_discovery)
S3method(bundle,domainogram_discovery)
S3method(bundle,saddle_discovery)
S3method(bundle,virtual4C_discovery)
S3method(expnames,ARMLA_discovery)
S3method(expnames,IIT_discovery)
S3method(expnames,RCP_discovery)
S3method(expnames,chrommat_discovery)
S3method(expnames,contacts)
S3method(expnames,default)
S3method(expnames,genomescore_discovery)
S3method(expnames,list)
S3method(expnames,saddle_discovery)
S3method(ggplot_add,genomescore_discovery)
S3method(ggplot_add,mark_layer)
S3method(ggplot_add,track_layer)
S3method(image,contacts_matrix)
S3method(persp,APA_discovery)
S3method(persp,PESCAn_discovery)
S3method(plot,APA_discovery)
S3method(plot,ARA_discovery)
S3method(plot,ATA_discovery)
S3method(plot,CSCAn_discovery)
S3method(plot,CS_discovery)
S3method(plot,DI_discovery)
S3method(plot,IIT_discovery)
S3method(plot,IS_discovery)
S3method(plot,PESCAn_discovery)
S3method(plot,RCP_discovery)
S3method(plot,domainogram_discovery)
S3method(plot,saddle_discovery)
S3method(plot,virtual4C_discovery)
S3method(print,ARMLA_discovery)
S3method(print,CS_discovery)
S3method(print,DI_discovery)
S3method(print,IIT_discovery)
S3method(print,IS_discovery)
S3method(print,RCP_discovery)
S3method(print,anchors)
S3method(print,chrommat_discovery)
S3method(print,contacts)
S3method(print,domainogram_discovery)
S3method(print,saddle_discovery)
S3method(print,virtual4C_discovery)
S3method(pyramid,contacts)
S3method(pyramid,contacts_matrix)
S3method(pyramid,default)
S3method(pyramid,matrix)
S3method(quantify,APA_discovery)
S3method(quantify,ARA_discovery)
S3method(quantify,ATA_discovery)
S3method(quantify,CSCAn_discovery)
S3method(quantify,IIT_discovery)
S3method(quantify,PESCAn_discovery)
S3method(quantify,default)
S3method(quantify,saddle_discovery)
S3method(range,contacts)
S3method(range,discovery)
S3method(resolution,contact_matrix)
S3method(resolution,contacts)
S3method(resolution,default)
S3method(resolution,discovery)
S3method(resolution,list)
S3method(subset,ARMLA_discovery)
S3method(subset,contacts)
S3method(unbundle,ARMLA_discovery)
S3method(unbundle,CS_discovery)
S3method(unbundle,DI_discovery)
S3method(unbundle,IIT_discovery)
S3method(unbundle,IS_discovery)
S3method(unbundle,RCP_discovery)
S3method(unbundle,chrommat_discovery)
S3method(unbundle,domainogram_discovery)
S3method(unbundle,saddle_discovery)
S3method(unbundle,virtual4C_discovery)
S3method(visualise,APA_discovery)
S3method(visualise,ARA_discovery)
S3method(visualise,ATA_discovery)
S3method(visualise,CSCAn_discovery)
S3method(visualise,CS_discovery)
S3method(visualise,DI_discovery)
S3method(visualise,IIT_discovery)
S3method(visualise,IS_discovery)
S3method(visualise,PESCAn_discovery)
S3method(visualise,RCP_discovery)
S3method(visualise,chrommat_discovery)
S3method(visualise,default)
S3method(visualise,domainogram_discovery)
S3method(visualise,saddle_discovery)
S3method(visualise,virtual4C_discovery)
export("expnames<-")
export(APA)
export(ARA)
export(ATA)
export(CSCAn)
export(HiCseg.callTAD)
export(PESCAn)
export(RCP)
export(RCPlfc)
export(add_bed_graph)
export(add_bed_track)
export(add_ctcf_sites)
export(add_loops)
export(add_tads)
export(anchors_APA)
export(anchors_ARA)
export(anchors_ATA)
export(anchors_CSCAn)
export(anchors_PESCAn)
export(anchors_extendedloops)
export(anchors_filter_oob)
export(anchors_shift)
export(as_anchors)
export(as_track)
export(bed2idx)
export(bundle)
export(call_TAD_insulation)
export(centromere.telomere.analysis)
export(chromosome_matrix)
export(cis_trans)
export(compartment_matrixplot)
export(compartment_score)
export(direct_index)
export(draw.centromere.telomere)
export(erase_GENOVA_cache)
export(expnames)
export(find_centromeres)
export(get_test_data)
export(hic_matrixplot)
export(insulation_domainogram)
export(insulation_matrixplot)
export(insulation_score)
export(intra_inter_TAD)
export(is_anchors)
export(load_contacts)
export(log2overmean)
export(log2overmedian)
export(pyramid)
export(pyramid_difference)
export(quantify)
export(read_bedpe)
export(rep_mat_lookup)
export(resolution)
export(saddle)
export(scale_altfill_continuous)
export(scale_colour_GENOVA)
export(scale_colour_GENOVA_div)
export(scale_fill_GENOVA)
export(scale_fill_GENOVA_div)
export(select_subset)
export(shuffleHiC)
export(sign_compartmentscore)
export(sync_indices)
export(tornado_aggregate)
export(tornado_insulation)
export(trans.compartment.plot)
export(trans_matrixplot)
export(unbundle)
export(virtual_4C)
export(visualise)
import(data.table)
import(grDevices)
import(graphics)
import(methods)
import(stats)
import(utils)
importFrom(ggplot2,ggplot_add)