ENCODE experiment and file queries: 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].

Retrieve ENCODE experiment details by accession¶

dnakit.encode.get_experiment(accession, *, verbose=True)

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

Retrieve live ENCODE filter counts¶

dnakit.encode.get_facets(search_type='Experiment', assay_title=None, organism=None, organ=None, biosample_type=None, *, verbose=True)

Parameter	Type	Required / default	Description and constraints
`search_type`	str	'Experiment'	Object type ("Experiment" or "File")
`assay_title`	str \| None	None	Pre-filter by assay type
`organism`	str \| None	None	Pre-filter by organism
`organ`	str \| None	None	Pre-filter by organ
`biosample_type`	str \| None	None	Pre-filter by biosample type
`verbose`	bool	True	Show DNAKit progress messages without changing results.

Retrieve ENCODE file details¶

dnakit.encode.get_file_info(accession, *, verbose=True)

Parameter	Type	Required / default	Description and constraints
`accession`	str	Required	File accession ID (e.g., "ENCFF635JIA")
`verbose`	bool	True	Show DNAKit progress messages without changing results.

Retrieve available ENCODE search filters¶

dnakit.encode.get_metadata(metadata_type, *, verbose=True)

Parameter	Type	Required / default	Description and constraints
`metadata_type`	Literal['assays', 'organisms', 'organs', 'biosample_types', 'file_formats', 'output_types', 'output_categories', 'assemblies', 'life_stages', 'replication_types', 'statuses', 'file_statuses']	Required	Type of metadata to retrieve. Options: - "assays": Available assay types (Histone ChIP-seq, ATAC-seq, total RNA-seq, etc.) - "organisms": Available organisms (Homo sapiens, Mus musculus, etc.) - "organs": Available organ/tissue systems (pancreas, brain, liver, etc.) - "biosample_types": Biosample classifications (tissue, cell line, primary cell, etc.) - "file_formats": File format types (fastq, bam, bed, bigWig, etc.) - "output_types": Output data types (reads, peaks, signal, etc.) - "output_categories": Output categories (raw data, alignment, signal, etc.) - "assemblies": Genome assemblies (GRCh38, hg19, mm10, etc.) - "life_stages": Life stages (embryonic, adult, child, etc.) - "replication_types": Replication types (isogenic, anisogenic, unreplicated) - "statuses": Experiment statuses (released, archived, etc.) - "file_statuses": File statuses (released, archived, in progress, etc.)
`verbose`	bool	True	Show DNAKit progress messages without changing results.

List files belonging to an ENCODE experiment¶

dnakit.encode.list_files(experiment_accession, file_format=None, file_type=None, output_type=None, output_category=None, assembly=None, status=None, preferred_default=None, limit=200, *, verbose=True)

Parameter	Type	Required / default	Description and constraints
`experiment_accession`	str	Required	ENCODE experiment accession (e.g., "ENCSR133RZO")
`file_format`	str \| None	None	Filter by format ("fastq", "bam", "bed", "bigWig", "bigBed", etc.)
`file_type`	str \| None	None	Filter by specific type ("bed narrowPeak", "bed broadPeak", etc.)
`output_type`	str \| None	None	Filter by output type ("reads", "peaks", "signal", etc.)
`output_category`	str \| None	None	Filter by category ("raw data", "alignment", "signal", "annotation")
`assembly`	str \| None	None	Filter by genome assembly ("GRCh38", "hg19", "mm10")
`status`	str \| None	None	Filter by status ("released", "archived", "in progress")
`preferred_default`	bool \| None	None	If True, return only default/recommended files
`limit`	int	200	Max files to return (default 200)
`verbose`	bool	True	Show DNAKit progress messages without changing results.

Search ENCODE experiments by experimental conditions¶

dnakit.encode.search_experiments(assay_title=None, organism='Homo sapiens', organ=None, biosample_type=None, biosample_term_name=None, target=None, status='released', lab=None, award=None, assembly=None, replication_type=None, life_stage=None, sex=None, treatment=None, genetic_modification=None, perturbed=None, search_term=None, date_released_from=None, date_released_to=None, limit=25, offset=0, *, verbose=True)

Parameter	Type	Required / default	Description and constraints
`assay_title`	str \| None	None	Assay type (e.g., "Histone ChIP-seq", "ATAC-seq", "total RNA-seq")
`organism`	str	'Homo sapiens'	Species (default: "Homo sapiens"). Also: "Mus musculus"
`organ`	str \| None	None	Organ/tissue system (e.g., "pancreas", "brain", "liver")
`biosample_type`	str \| None	None	Sample classification ("tissue", "cell line", "primary cell", "organoid")
`biosample_term_name`	str \| None	None	Specific cell/tissue name (e.g., "GM12878", "HepG2", "pancreas")
`target`	str \| None	None	ChIP/CUT&RUN target (e.g., "H3K27me3", "CTCF", "p300")
`status`	str	'released'	Data status (default: "released"). Also: "archived", "revoked"
`lab`	str \| None	None	Submitting lab name
`award`	str \| None	None	Funding project
`assembly`	str \| None	None	Genome assembly (e.g., "GRCh38", "mm10")
`replication_type`	str \| None	None	"isogenic", "anisogenic", or "unreplicated"
`life_stage`	str \| None	None	"embryonic", "postnatal", "child", "adult"
`sex`	str \| None	None	"male", "female", "mixed"
`treatment`	str \| None	None	Treatment name if perturbation experiment
`genetic_modification`	str \| None	None	Modification type ("CRISPR", "RNAi")
`perturbed`	bool \| None	None	True for perturbation experiments only
`search_term`	str \| None	None	Free text search across all fields
`date_released_from`	str \| None	None	Start date (YYYY-MM-DD) for date range filter
`date_released_to`	str \| None	None	End date (YYYY-MM-DD) for date range filter
`limit`	int	25	Max results to return (default 25, use larger for comprehensive searches)
`offset`	int	0	Skip first N results (for pagination)
`verbose`	bool	True	Show DNAKit progress messages without changing results.

Search ENCODE files using experiment and file filters¶

dnakit.encode.search_files(file_format=None, file_type=None, output_type=None, output_category=None, assembly=None, assay_title=None, organism=None, organ=None, biosample_type=None, target=None, status='released', preferred_default=None, search_term=None, limit=25, offset=0, *, verbose=True)

Parameter	Type	Required / default	Description and constraints
`file_format`	str \| None	None	File format ("fastq", "bam", "bed", "bigWig", etc.)
`file_type`	str \| None	None	Specific file type ("bed narrowPeak", "bed broadPeak", etc.)
`output_type`	str \| None	None	Output type ("reads", "peaks", "signal", etc.)
`output_category`	str \| None	None	Output category ("raw data", "alignment", "signal", "annotation")
`assembly`	str \| None	None	Genome assembly ("GRCh38", "hg19", "mm10")
`assay_title`	str \| None	None	Filter by assay type of parent experiment
`organism`	str \| None	None	Filter by organism of parent experiment
`organ`	str \| None	None	Filter by organ of parent experiment
`biosample_type`	str \| None	None	Filter by biosample type ("tissue", "cell line", etc.)
`target`	str \| None	None	Filter by ChIP/CUT&RUN target
`status`	str	'released'	File status (default: "released")
`preferred_default`	bool \| None	None	If True, only default/recommended files
`search_term`	str \| None	None	Free text search
`limit`	int	25	Max results (default 25)
`offset`	int	0	Skip first N results (pagination)
`verbose`	bool	True	Show DNAKit progress messages without changing results.