# DeepBlueR

## Documentation for package ‘DeepBlueR’ version 1.4.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

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