DeepBlueR

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Documentation for package ‘DeepBlueR’ version 1.19.1

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DeepBlueCommand DeepBlueCommand class
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-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_genes list_genes
deepblue_list_gene_models list_gene_models
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