encode-toolkit

Search ENCODE experiments with comprehensive filters.

Examples:

• Find all Histone ChIP-seq on human pancreas tissue: assay_title="Histone ChIP-seq", organ="pancreas", biosample_type="tissue"

• Find ATAC-seq on human brain: assay_title="ATAC-seq", organ="brain"

• Find RNA-seq on GM12878 cell line: assay_title="RNA-seq", biosample_term_name="GM12878"

• Find ChIP-seq targeting H3K27me3: assay_title="Histone ChIP-seq", target="H3K27me3"

• Find all mouse liver experiments: organism="Mus musculus", organ="liver"

• Free text search: search_term="CRISPR screen pancreatic"

Common assay_title values: "Histone ChIP-seq", "TF ChIP-seq", "ATAC-seq", "DNase-seq", "RNA-seq", "total RNA-seq", "WGBS", "Hi-C", "CUT&RUN", "CUT&Tag", "STARR-seq", "MPRA", "eCLIP", "CRISPR screen"

Common organ values: "pancreas", "liver", "brain", "heart", "kidney", "lung", "intestine", "skin of body", "blood", "spleen", "thymus"

biosample_type values: "tissue", "cell line", "primary cell", "in vitro differentiated cells", "organoid"

WHEN TO USE: Use as the primary entry point when users want to find experiments. Start with encode_get_facets if unsure what filters to use. RELATED TOOLS: encode_get_facets, encode_get_metadata, encode_search_files

Args: assay_title: Assay type (e.g., "Histone ChIP-seq", "ATAC-seq", "RNA-seq") organism: Species (default: "Homo sapiens"). Also: "Mus musculus" organ: Organ/tissue system (e.g., "pancreas", "brain", "liver") biosample_type: Sample classification ("tissue", "cell line", "primary cell", "organoid") biosample_term_name: Specific cell/tissue name (e.g., "GM12878", "HepG2", "pancreas") target: ChIP/CUT&RUN target (e.g., "H3K27me3", "CTCF", "p300") status: Data status (default: "released"). Also: "archived", "revoked" lab: Submitting lab name award: Funding project assembly: Genome assembly (e.g., "GRCh38", "mm10") replication_type: "isogenic", "anisogenic", or "unreplicated" life_stage: "embryonic", "postnatal", "child", "adult" sex: "male", "female", "mixed" treatment: Treatment name if perturbation experiment genetic_modification: Modification type ("CRISPR", "RNAi") perturbed: True for perturbation experiments only search_term: Free text search across all fields date_released_from: Start date (YYYY-MM-DD) for date range filter date_released_to: End date (YYYY-MM-DD) for date range filter limit: Max results to return (default 25, use larger for comprehensive searches) offset: Skip first N results (for pagination)

Returns: JSON with experiment results, total count, and pagination info.