Display functions defined through the bedhost API and their corresponding parameters.
# S4 method for class 'BEDbase'
operations(x, ..., .deprecated = FALSE)list() API endpoints
bedbase <- BEDbase()
#> 663721 BED files available.
operations(bedbase)
#> $landing_page__get
#> landing_page__get
#> Landing Page
#>
#> Parameters:
#>
#> $index_v1_get
#> index_v1_get
#> API intro page
#> Description:
#> Display the index UI page
#>
#> Parameters:
#>
#> $get_assays_list_v1_assays_get
#> get_assays_list_v1_assays_get
#> Get available assays
#> Description:
#> Returns available assays
#>
#> Parameters:
#>
#> $analyze_reference_genome_v1_bed_analyze_genome_post
#> analyze_reference_genome_v1_bed_analyze_genome_post
#> Analyze reference genome for bed file
#> Description:
#> Provide length of the chromosomes for a reference genome, and return
#> reference genome validation results for a bed file
#>
#> Parameters:
#> bed_file (object)
#>
#> $embed_bed_file_v1_bed_embed_post
#> embed_bed_file_v1_bed_embed_post
#> Get embeddings for a bed file.
#> Description:
#> Create embedding for bed file
#>
#> Parameters:
#> file (string)
#>
#> $get_example_bed_record_v1_bed_example_get
#> get_example_bed_record_v1_bed_example_get
#> Get example BED record metadata
#> Description:
#> Get metadata for an example BED record.
#>
#> Parameters:
#>
#> $list_beds_v1_bed_list_get
#> list_beds_v1_bed_list_get
#> Paged list of all BED records
#> Description:
#> Returns list of BED files in the database with optional filters.
#>
#> Parameters:
#> limit (integer)
#> Limit (1-10000), default 1000
#> offset (integer)
#> genome (string)
#> filter by genome of the bed file. e.g. 'hg38'
#> bed_compliance (string)
#> filter by bed type. e.g. 'bed6+4'
#>
#> $missing_plots_v1_bed_missing_plots_get
#> missing_plots_v1_bed_missing_plots_get
#> Get missing plots for a bed file.
#> Description:
#> Get missing plots for a bed file
#>
#> example -> plot_id: gccontent
#>
#> Parameters:
#> plot_id (string)
#>
#> $bed_to_bed_search_v1_bed_search_bed_post
#> bed_to_bed_search_v1_bed_search_bed_post
#> Search for similar bed files
#>
#> Parameters:
#> limit (integer)
#> offset (integer)
#> file (string)
#>
#> $exact_search_v1_bed_search_exact_get
#> exact_search_v1_bed_search_exact_get
#> Search for exact match of metadata in bed files
#>
#> Parameters:
#> query (string)
#> genome ()
#> assay ()
#> limit (integer)
#> offset (integer)
#>
#> $text_to_bed_search_v1_bed_search_text_get
#> text_to_bed_search_v1_bed_search_text_get
#> Search for a BedFile
#> Description:
#> Search for a BedFile by a text query.
#>
#> By default, it searches in the 'hg38' genome. To search in a
#> different genome, specify the `genome` parameter. eg. mm10 Example:
#> query="cancer"
#>
#> Parameters:
#> query (string)
#> genome ()
#> assay ()
#> limit (integer)
#> offset (integer)
#> test_request (boolean)
#>
#> $umap_bed_file_v1_bed_umap_post
#> umap_bed_file_v1_bed_umap_post
#> Get embeddings for a bed file.
#> Description:
#> Create embedding for bed file
#>
#> Parameters:
#> file (string)
#>
#> $get_bed_embedding_v1_bed__bed_id__embedding_get
#> get_bed_embedding_v1_bed__bed_id__embedding_get
#> Get embeddings for a single BED record
#> Description:
#> Returns embeddings for a single BED record.
#>
#> Parameters:
#> bed_id (string)
#> BED digest
#>
#> $get_ref_gen_results_v1_bed__bed_id__genome_stats_get
#> get_ref_gen_results_v1_bed__bed_id__genome_stats_get
#> Get reference genome validation results
#> Description:
#> Return reference genome validation results for a bed file Example:
#> bed: 0dcdf8986a72a3d85805bbc9493a1302
#>
#> Parameters:
#> bed_id (string)
#>
#> $get_bed_metadata_v1_bed__bed_id__metadata_get
#> get_bed_metadata_v1_bed__bed_id__metadata_get
#> Get metadata for a single BED record
#> Description:
#> Example bed_id: bbad85f21962bb8d972444f7f9a3a932
#>
#> Parameters:
#> bed_id (string)
#> BED digest
#> full ()
#> Return full record with stats, plots, files and metadata
#> test_request (boolean)
#>
#> $get_bed_classification_v1_bed__bed_id__metadata_classification_get
#> get_bed_classification_v1_bed__bed_id__metadata_classification_get
#> Get classification of single BED file
#> Description:
#> Example bed_id: bbad85f21962bb8d972444f7f9a3a932
#>
#> Parameters:
#> bed_id (string)
#> BED digest
#>
#> $get_bed_files_v1_bed__bed_id__metadata_files_get
#> get_bed_files_v1_bed__bed_id__metadata_files_get
#> Get metadata for a single BED record
#> Description:
#> Example bed_id: bbad85f21962bb8d972444f7f9a3a932
#>
#> Parameters:
#> bed_id (string)
#> BED digest
#>
#> $get_bed_plots_v1_bed__bed_id__metadata_plots_get
#> get_bed_plots_v1_bed__bed_id__metadata_plots_get
#> Get plots for a single BED record
#> Description:
#> Example bed_id: bbad85f21962bb8d972444f7f9a3a932
#>
#> Parameters:
#> bed_id (string)
#> BED digest
#>
#> $get_bed_stats_v1_bed__bed_id__metadata_stats_get
#> get_bed_stats_v1_bed__bed_id__metadata_stats_get
#> Get stats for a single BED record
#> Description:
#> Example bed_id: bbad85f21962bb8d972444f7f9a3a932
#>
#> Parameters:
#> bed_id (string)
#> BED digest
#>
#> $get_bed_neighbours_v1_bed__bed_id__neighbours_get
#> get_bed_neighbours_v1_bed__bed_id__neighbours_get
#> Get nearest neighbours for a single BED record
#> Description:
#> Returns most similar BED files in the database. Example bed_id:
#> bbad85f21962bb8d972444f7f9a3a932
#>
#> Parameters:
#> bed_id (string)
#> BED digest
#> limit (integer)
#> offset (integer)
#>
#> $get_bed_og_image_v1_bed__bed_id__og_image_get
#> get_bed_og_image_v1_bed__bed_id__og_image_get
#> Get Open Graph preview image for a BED record
#> Description:
#> Returns a 1200x630 PNG card with stats for link previews. Example
#> bed_id: bbad85f21962bb8d972444f7f9a3a932
#>
#> Parameters:
#> bed_id (string)
#> BED digest
#>
#> $get_regions_for_bedfile_v1_bed__bed_id__regions__chr_num__get
#> get_regions_for_bedfile_v1_bed__bed_id__regions__chr_num__get
#> Get regions from a BED file that overlap a query region.
#> Description:
#> Returns the queried regions with provided ID and optional query
#> parameters
#>
#> Parameters:
#> bed_id (string)
#> BED digest
#> chr_num (string)
#> Chromosome number
#> start ()
#> query range: start coordinate
#> end ()
#> query range: start coordinate
#>
#> $get_tokens_v1_bed__bed_id__tokens__universe_id__get
#> get_tokens_v1_bed__bed_id__tokens__universe_id__get
#> Get tokenized of bed file
#> Description:
#> Return univers of bed file Example: bed:
#> 0dcdf8986a72a3d85805bbc9493a1302 | universe:
#> 58dee1672b7e581c8e1312bd4ca6b3c7
#>
#> Parameters:
#> bed_id (string)
#> universe_id (string)
#>
#> $get_tokens_info_v1_bed__bed_id__tokens__universe_id__info_get
#> get_tokens_info_v1_bed__bed_id__tokens__universe_id__info_get
#> Get link to tokenized bed file
#> Description:
#> Return link to tokenized bed file Example: bed:
#> 0dcdf8986a72a3d85805bbc9493a1302 | universe:
#> 58dee1672b7e581c8e1312bd4ca6b3c7
#>
#> Parameters:
#> bed_id (string)
#> universe_id (string)
#>
#> $create_bedset_v1_bedset_create_post
#> create_bedset_v1_bedset_create_post
#> Create Bedset
#> Description:
#> Create a new bedset by providing registry path to the PEPhub project
#>
#> Parameters:
#> registry_path (string)
#>
#> $get_example_bedset_record_v1_bedset_example_get
#> get_example_bedset_record_v1_bedset_example_get
#> Get metadata for an example BEDset record
#>
#> Parameters:
#>
#> $list_bedsets_v1_bedset_list_get
#> list_bedsets_v1_bedset_list_get
#> Paged list of all BEDset records
#> Description:
#> Returns a list of BEDset records in the database with optional
#> filters and search.
#>
#> Parameters:
#> query ()
#> limit (integer)
#> offset (integer)
#> test_request (boolean)
#>
#> $get_bedfiles_in_bedset_v1_bedset__bedset_id__bedfiles_get
#> get_bedfiles_in_bedset_v1_bedset__bedset_id__bedfiles_get
#> Get Bedfiles In Bedset
#> Description:
#> Example bed_id: gse218680
#>
#> Parameters:
#> bedset_id (string)
#>
#> $get_bedset_metadata_v1_bedset__bedset_id__metadata_get
#> get_bedset_metadata_v1_bedset__bedset_id__metadata_get
#> Get all metadata for a single BEDset record
#> Description:
#> Example bed_id: gse218680
#>
#> Parameters:
#> bedset_id (string)
#> full (boolean)
#> test_request (boolean)
#>
#> $get_bedset_plots_handler_v1_bedset__bedset_id__metadata_plots_get
#> get_bedset_plots_handler_v1_bedset__bedset_id__metadata_plots_get
#> Get plots for single bedset record
#> Description:
#> Example bed_id: gse218680
#>
#> Parameters:
#> bedset_id (string)
#>
#> $get_bedset_stats_handler_v1_bedset__bedset_id__metadata_stats_get
#> get_bedset_stats_handler_v1_bedset__bedset_id__metadata_stats_get
#> Get stats for a single BEDSET record
#> Description:
#> Example bed_id: gse218680
#>
#> Parameters:
#> bedset_id (string)
#>
#> $get_bedset_pep_v1_bedset__bedset_id__pep_get
#> get_bedset_pep_v1_bedset__bedset_id__pep_get
#> Download PEP project for a single BEDset record
#> Description:
#> Example bed_id: gse218680
#>
#> Parameters:
#> bedset_id (string)
#>
#> $get_track_hub_bedset_v1_bedset__bedset_id__track_hub_get
#> get_track_hub_bedset_v1_bedset__bedset_id__track_hub_get
#> Get Track Hub Bedset
#> Description:
#> Generate track hub files for the BED set
#>
#> Parameters:
#> bedset_id (string)
#>
#> $get_track_hub_bedset_v1_bedset__bedset_id__track_hub_head
#> get_track_hub_bedset_v1_bedset__bedset_id__track_hub_head
#> Get Track Hub Bedset
#> Description:
#> Generate track hub files for the BED set
#>
#> Parameters:
#> bedset_id (string)
#>
#> $get_detailed_stats_v1_detailed_stats_get
#> get_detailed_stats_v1_detailed_stats_get
#> Get detailed statistics for BEDbase platform, including number of files for each genome
#> Description:
#> Returns detailed statistics
#>
#> Parameters:
#> concise (boolean)
#>
#> $get_detailed_usage_v1_detailed_usage_get
#> get_detailed_usage_v1_detailed_usage_get
#> Get detailed usage statistics for BEDbase platform
#> Description:
#> Returns detailed usage statistics
#>
#> Parameters:
#>
#> $changelog_v1_docs_changelog_get
#> changelog_v1_docs_changelog_get
#> Release notes
#>
#> Parameters:
#>
#> $get_bed_exports_v1_exports_get
#> get_bed_exports_v1_exports_get
#> Index of published bulk metadata exports (newest first)
#> Description:
#> Return the index of bulk metadata export artifacts published to S3,
#> newest first. ``file_path`` is rewritten to the absolute HTTPS CDN
#> URL. Consumers should resolve the current snapshot through this
#> endpoint rather than constructing or hardcoding a filename, since
#> artifacts are dated and immutable.
#>
#> Declared ``def`` (not ``async def``) so the blocking database query
#> runs in a threadpool instead of stalling the event loop.
#>
#> Parameters:
#> limit (integer)
#> Limit (1-10000), default 1000
#> offset (integer)
#>
#> $get_analysis_files_v1_files_get
#> get_analysis_files_v1_files_get
#> Index of standalone analysis files (newest first)
#> Description:
#> Return the index of standalone analysis files (openSignalMatrix,
#> models, other analysis inputs) stored in S3, newest first. These
#> files are global; they are not tied to any bed file or bedset.
#> ``file_path`` is rewritten to the absolute HTTPS CDN URL.
#>
#> Declared ``def`` (not ``async def``) so the blocking database query
#> runs in a threadpool instead of stalling the event loop.
#>
#> Parameters:
#> file_type ()
#> Filter by file type
#> genome ()
#> Filter by genome/assembly
#> tag ()
#> Filter by a single tag
#> limit (integer)
#> Limit (1-10000), default 1000
#> offset (integer)
#>
#> $redirect_to_download_v1_files__file_path__get
#> redirect_to_download_v1_files__file_path__get
#> Redirect To Download
#>
#> Parameters:
#> file_path (string)
#> test_request (boolean)
#>
#> $get_genomes_list_v1_genomes_get
#> get_genomes_list_v1_genomes_get
#> Get available genomes
#> Description:
#> Returns available genomes
#>
#> Parameters:
#>
#> $list_export_drs_objects_v1_objects_exports_get
#> list_export_drs_objects_v1_objects_exports_get
#> List published bulk-metadata exports as DRS objects (newest first)
#> Description:
#> Enumerate every published bulk-metadata export artifact as a GA4GH
#> DRS object, newest first.
#>
#> The DRS object-id of an export is its bare filename (the basename of
#> the ``bed_snapshots.file_path`` S3 key), e.g.
#> ``bedbase_metadata_2026_08_03.parquet``. Resolve a single object at
#> ``GET /v1/objects/exports/{object_id}``.
#>
#> Declared ``def`` (not ``async def``) so the blocking database query
#> runs in a threadpool instead of stalling the event loop.
#>
#> Parameters:
#>
#> $get_export_drs_object_metadata_v1_objects_exports__object_id__get
#> get_export_drs_object_metadata_v1_objects_exports__object_id__get
#> Get DRS object metadata for a bulk-metadata export
#> Description:
#> Return GA4GH DRS metadata for a single published bulk-metadata
#> export.
#>
#> ``object_id`` is the export's bare filename (the basename of the
#> ``bed_snapshots.file_path`` S3 key), e.g.
#> ``bedbase_metadata_2026_08_03.parquet``. The id round-trips: the
#> resolved ``bed_snapshots`` row is the newest whose ``file_path``
#> basename equals ``object_id``.
#>
#> Declared ``def`` (not ``async def``) so the blocking database query
#> runs in a threadpool instead of stalling the event loop.
#>
#> Parameters:
#> object_id (string)
#>
#> $list_analysis_file_drs_objects_v1_objects_files_get
#> list_analysis_file_drs_objects_v1_objects_files_get
#> List standalone analysis files as DRS objects (newest first)
#> Description:
#> Enumerate every standalone analysis file as a GA4GH DRS object,
#> newest first.
#>
#> The DRS object-id of an analysis file is its bare filename (the
#> basename of the ``analysis_files.file_path`` S3 key). Resolve a
#> single object at ``GET /v1/objects/files/{object_id}``.
#>
#> Declared ``def`` (not ``async def``) so the blocking database query
#> runs in a threadpool instead of stalling the event loop.
#>
#> Parameters:
#>
#> $get_analysis_file_drs_object_metadata_v1_objects_files__object_id__get
#> get_analysis_file_drs_object_metadata_v1_objects_files__object_id__get
#> Get DRS object metadata for a standalone analysis file
#> Description:
#> Return GA4GH DRS metadata for a single standalone analysis file.
#>
#> ``object_id`` is the file's bare filename (the basename of the
#> ``analysis_files.file_path`` S3 key). The id round-trips: the
#> resolved ``analysis_files`` row is the newest whose ``file_path``
#> basename equals ``object_id``.
#>
#> Declared ``def`` (not ``async def``) so the blocking database query
#> runs in a threadpool instead of stalling the event loop.
#>
#> Parameters:
#> object_id (string)
#>
#> $get_drs_object_metadata_v1_objects__object_id__get
#> get_drs_object_metadata_v1_objects__object_id__get
#> Get DRS object metadata
#> Description:
#> Returns metadata about a DrsObject.
#>
#> Parameters:
#> object_id (string)
#>
#> $get_object_bytes_url_v1_objects__object_id__access__access_id__get
#> get_object_bytes_url_v1_objects__object_id__access__access_id__get
#> Get URL where you can retrieve files
#> Description:
#> Returns a URL that can be used to fetch the bytes of a DrsObject.
#>
#> Parameters:
#> object_id (string)
#> access_id (string)
#>
#> $get_object_bytes_v1_objects__object_id__access__access_id__bytes_get
#> get_object_bytes_v1_objects__object_id__access__access_id__bytes_get
#> Download actual file
#> Description:
#> Returns the bytes of a DrsObject.
#>
#> Parameters:
#> object_id (string)
#> access_id (string)
#>
#> $get_object_thumbnail_v1_objects__object_id__access__access_id__thumbnail_get
#> get_object_thumbnail_v1_objects__object_id__access__access_id__thumbnail_get
#> Download thumbnail file
#> Description:
#> Returns the bytes of a thumbnail of a DrsObject
#>
#> Parameters:
#> object_id (string)
#> access_id (string)
#>
#> $service_info_v1_service_info_get
#> service_info_v1_service_info_get
#> GA4GH service info
#> Description:
#> Returns information about this service, such as versions, name, etc.
#>
#> Parameters:
#>
#> $get_bedbase_db_stats_v1_stats_get
#> get_bedbase_db_stats_v1_stats_get
#> Get summary statistics for BEDbase platform
#> Description:
#> Returns statistics
#>
#> Parameters:
#>