DeepBlueCommand-class   DeepBlueCommand class
deepblue_aggregate      aggregate
deepblue_batch_export_results
                        batch_export_results
deepblue_binning        binning
deepblue_cache_status   Report on the cache size and status
deepblue_cancel_request
                        cancel_request
deepblue_chromosomes    chromosomes
deepblue_clear_cache    Clear cache
deepblue_collection_experiments_count
                        collection_experiments_count
deepblue_commands       commands
deepblue_count_gene_ontology_terms
                        count_gene_ontology_terms
deepblue_count_regions
                        count_regions
deepblue_coverage       coverage
deepblue_delete_request_from_cache
                        Delete a specific request from the cache
deepblue_diff           diff
deepblue_distinct_column_values
                        distinct_column_values
deepblue_download_request_data
                        deepblue_download_request_data
deepblue_download_request_data,DeepBlueCommand-method
                        deepblue_download_request_data
deepblue_echo           echo
deepblue_enrich_regions_fast
                        enrich_regions_fast
deepblue_enrich_regions_go_terms
                        enrich_regions_go_terms
deepblue_enrich_regions_overlap
                        enrich_regions_overlap
deepblue_export_bed     Export GenomicRanges result as BED file
deepblue_export_meta_data
                        Export meta data as tab delimited file
deepblue_export_tab     Export a DeepBlue result as ordinary tab
                        delimited file
deepblue_extend         extend
deepblue_extract_ids    extract_ids
deepblue_extract_names
                        extract_names
deepblue_faceting_experiments
                        faceting_experiments
deepblue_filter_regions
                        filter_regions
deepblue_find_motif     find_motif
deepblue_flank          flank
deepblue_format_object_size
                        Format byte size as human readable units
deepblue_get_biosource_children
                        get_biosource_children
deepblue_get_biosource_parents
                        get_biosource_parents
deepblue_get_biosource_related
                        get_biosource_related
deepblue_get_biosource_synonyms
                        get_biosource_synonyms
deepblue_get_db         Sets up the DeepBlueR cache and returns a
                        filehash db object
deepblue_get_experiments_by_query
                        get_experiments_by_query
deepblue_get_regions    get_regions
deepblue_get_request_data
                        get_request_data
deepblue_info           info
deepblue_input_regions
                        input_regions
deepblue_intersection   intersection
deepblue_is_biosource   is_biosource
deepblue_liftover       Lift over region results between Genome
                        Assemblies used in DeepBlue
deepblue_list_annotations
                        list_annotations
deepblue_list_biosources
                        list_biosources
deepblue_list_cached_requests
                        List cached requests
deepblue_list_column_types
                        list_column_types
deepblue_list_epigenetic_marks
                        list_epigenetic_marks
deepblue_list_experiments
                        list_experiments
deepblue_list_expressions
                        list_expressions
deepblue_list_gene_models
                        list_gene_models
deepblue_list_genes     list_genes
deepblue_list_genomes   list_genomes
deepblue_list_in_use    list_in_use
deepblue_list_projects
                        list_projects
deepblue_list_recent_experiments
                        list_recent_experiments
deepblue_list_requests
                        list_requests
deepblue_list_samples   list_samples
deepblue_list_similar_biosources
                        list_similar_biosources
deepblue_list_similar_epigenetic_marks
                        list_similar_epigenetic_marks
deepblue_list_similar_experiments
                        list_similar_experiments
deepblue_list_similar_genomes
                        list_similar_genomes
deepblue_list_similar_projects
                        list_similar_projects
deepblue_list_similar_techniques
                        list_similar_techniques
deepblue_list_techniques
                        list_techniques
deepblue_merge_queries
                        merge_queries
deepblue_meta_data_to_table
                        Convert XML structured meta data to table
                        format
deepblue_name_to_id     name_to_id
deepblue_options        options
deepblue_overlap        overlap
deepblue_preview_experiment
                        preview_experiment
deepblue_query_cache    query_cache
deepblue_query_experiment_type
                        query_experiment_type
deepblue_reset_options
                        Reset DeepBlueR options
deepblue_score_matrix   score_matrix
deepblue_search         search
deepblue_select_annotations
                        select_annotations
deepblue_select_column
                        select column
deepblue_select_experiments
                        select_experiments
deepblue_select_expressions
                        select_expressions
deepblue_select_genes   select_genes
deepblue_select_regions
                        select_regions
deepblue_tiling_regions
                        tiling_regions
deepblue_wait_request   deepblue_wait_request
