Data partitioning: parameters and notes¶

See the tutorial for usage and examples.

Each function includes its purpose, API, inputs, outputs, example code and result description. Prepare any required credentials, local files and optional dependencies; remote results vary with database releases and query time.

ENCODE returns text: mostly JSON, but get_citations can return BibTeX/RIS and export_data can return CSV/TSV. Use json.loads() only for JSON. Tracking and credentials use ~/.dnakit-encode/; persistent credential storage needs dnakit[encode-credentials].

Compare ENCODE experiments for joint analysis compatibility¶

dnakit.encode.compare_experiments(accession1, accession2, *, verbose=True)

Parameter	Type	Required / default	Description and constraints
`accession1`	str	Required	First experiment accession (e.g., "ENCSR133RZO")
`accession2`	str	Required	Second experiment accession (e.g., "ENCSR000AKS")
`verbose`	bool	True	Show DNAKit progress messages without changing results.

Export tracked ENCODE experiments as a table¶

dnakit.encode.export_data(format='csv', assay_title=None, organism=None, organ=None, *, verbose=True)

Parameter	Type	Required / default	Description and constraints
`format`	Literal['csv', 'tsv', 'json']	'csv'	Output format: - "csv": Comma-separated values (default, for Excel/spreadsheets) - "tsv": Tab-separated values (for R, pandas) - "json": JSON array (for programmatic use)
`assay_title`	str \| None	None	Filter by assay type (partial match)
`organism`	str \| None	None	Filter by organism (partial match)
`organ`	str \| None	None	Filter by organ (partial match)
`verbose`	bool	True	Show DNAKit progress messages without changing results.

Retrieve publications and citations for tracked experiments¶

dnakit.encode.get_citations(accession=None, export_format='json', *, verbose=True)

Parameter	Type	Required / default	Description and constraints
`accession`	str \| None	None	Specific experiment accession. If None, returns all publications.
`export_format`	Literal['json', 'bibtex', 'ris']	'json'	Output format: - "json": Structured data (default) - "bibtex": BibTeX format for LaTeX - "ris": RIS format (Endnote, Zotero, Mendeley)
`verbose`	bool	True	Show DNAKit progress messages without changing results.

Retrieve derived-file provenance¶

dnakit.encode.get_provenance(file_path=None, source_accession=None, *, verbose=True)

Parameter	Type	Required / default	Description and constraints
`file_path`	str \| None	None	Get provenance for a specific derived file
`source_accession`	str \| None	None	List all files derived from a specific ENCODE accession
`verbose`	bool	True	Show DNAKit progress messages without changing results.

Retrieve external references linked to experiments¶

dnakit.encode.get_references(experiment_accession=None, reference_type=None, *, verbose=True)

Parameter	Type	Required / default	Description and constraints
`experiment_accession`	str \| None	None	Filter by specific experiment (optional)
`reference_type`	Literal['pmid', 'doi', 'nct_id', 'preprint_doi', 'geo_accession', 'other'] \| None	None	Filter by reference type (optional): "pmid", "doi", "nct_id", "preprint_doi", "geo_accession", "other"
`verbose`	bool	True	Show DNAKit progress messages without changing results.

Link an external reference to a tracked experiment¶

dnakit.encode.link_reference(experiment_accession, reference_type, reference_id, description='', *, verbose=True)

Parameter	Type	Required / default	Description and constraints
`experiment_accession`	str	Required	ENCODE experiment accession (e.g., "ENCSR133RZO")
`reference_type`	Literal['pmid', 'doi', 'nct_id', 'preprint_doi', 'geo_accession', 'other']	Required	Type of external reference: - "pmid": PubMed ID (e.g., "32728249") - "doi": DOI (e.g., "10.1038/s41586-020-2493-4") - "nct_id": ClinicalTrials.gov ID (e.g., "NCT04567890") - "preprint_doi": bioRxiv/medRxiv DOI - "geo_accession": GEO accession (e.g., "GSE123456") - "other": Any other identifier
`reference_id`	str	Required	The actual identifier value
`description`	str	''	Optional description of why this reference is linked
`verbose`	bool	True	Show DNAKit progress messages without changing results.

List locally tracked ENCODE experiments¶

dnakit.encode.list_tracked(assay_title=None, organism=None, organ=None, *, verbose=True)

Parameter	Type	Required / default	Description and constraints
`assay_title`	str \| None	None	Filter by assay type (partial match)
`organism`	str \| None	None	Filter by organism (partial match)
`organ`	str \| None	None	Filter by organ (partial match)
`verbose`	bool	True	Show DNAKit progress messages without changing results.

Record a derived file and its provenance¶

dnakit.encode.log_derived_file(file_path, source_accessions, description='', file_type='', tool_used='', parameters='', *, verbose=True)

Parameter	Type	Required / default	Description and constraints
`file_path`	str	Required	Path to the derived file you created
`source_accessions`	list[str]	Required	List of ENCODE accessions this file was derived from (experiment or file accessions, e.g., ["ENCSR133RZO", "ENCFF635JIA"])
`description`	str	''	What this derived file contains
`file_type`	str	''	Type of file (e.g., "filtered_peaks", "merged_signal", "differential")
`tool_used`	str	''	Tool/software used to create it (e.g., "bedtools intersect", "DESeq2")
`parameters`	str	''	Parameters or command used
`verbose`	bool	True	Show DNAKit progress messages without changing results.

Summarize tracked experiment collections by field¶

dnakit.encode.summarize_collection(assay_title=None, organism=None, organ=None, *, verbose=True)

Parameter	Type	Required / default	Description and constraints
`assay_title`	str \| None	None	Filter by assay type (partial match)
`organism`	str \| None	None	Filter by organism (partial match)
`organ`	str \| None	None	Filter by organ (partial match)
`verbose`	bool	True	Show DNAKit progress messages without changing results.

Track an ENCODE experiment and its provenance locally¶

dnakit.encode.track_experiment(accession, fetch_publications=True, fetch_pipelines=True, notes='', *, verbose=True)

Parameter	Type	Required / default	Description and constraints
`accession`	str	Required	ENCODE experiment accession (e.g., "ENCSR133RZO")
`fetch_publications`	bool	True	Also fetch and store publications/citations (default True)
`fetch_pipelines`	bool	True	Also fetch and store pipeline/analysis info (default True)
`notes`	str	''	Optional notes to attach to this experiment
`verbose`	bool	True	Show DNAKit progress messages without changing results.