NAMESPACE

# Generated by roxygen2: do not edit by hand

export(Create_QC_Output_Prefiltered_ATAC)
export(Create_QC_Output_Prefiltered_RNA)
export(FilterRawData_ATAC)
export(FilterRawData_RNA)
export(FindMappingAnchors)
export(FindMultiomeOverlap)
export(InferBatches)
export(InitialProcessing_ATAC)
export(InitialProcessing_RNA)
export(IntegrateByBatch_ATAC)
export(IntegrateByBatch_RNA)
export(LoadReferenceSPEEDI)
export(MajorityVote_ATAC)
export(MajorityVote_RNA)
export(MapCellTypes_ATAC)
export(MapCellTypes_RNA)
export(Read_ATAC)
export(Read_RNA)
export(RunDE_RNA)
export(RunFMD_RNA)
export(TransferRNALabels)
export(VisualizeIntegration)
export(addGeneIntegrationMatrix_SPEEDI)
export(create_SPEEDI_log_file)
export(create_pseudobulk_counts)
export(find_clusters_SPEEDI)
export(get_azimuth_references)
export(get_fmd_submission_url)
export(get_gene_check_url)
export(get_pbmc_reference_url)
export(get_references)
export(get_speedi_seed)
export(grab_hb_networks)
export(initialize_SPEEDI)
export(log_warning)
export(normalize_dir_path)
export(preliminary_check_for_SPEEDI_errors)
export(print_SPEEDI)
export(quit_SPEEDI)
export(run_SPEEDI)
export(run_downstream_analyses_RNA)
export(run_fmd_wrapper)
export(set_pbmc_reference_url)
export(set_speedi_seed)
export(stop_quietly)
import(ArchR)
importFrom(foreach,"%dopar%")