Expression, regulation and cancer 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.

ChIP-Atlas gene-based peak queries without peak_file return requires_data and a retrieval plan; interval overlaps require a BED with verified assembly. The enrichment entry returns requires_submission instructions, not computed enrichment statistics.

Browse the cBioPortal cancer study catalogue

dnakit.databases.c_bio_portal_get_cancer_studies(*, limit=None, offset=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
limit	integer	None	Number of studies to return in this page. The default of 20 covers only a small fraction of the catalogue; set it to the total_available reported in the response to retrieve every study.
offset	integer	None	0-based index of the first study to return, for paging through the catalogue. Applied client-side because the cBioPortal /studies endpoint ignores its own pageNumber parameter.
verbose	bool	True	Progress flag.

Retrieve cBioPortal gene information by Entrez ID

dnakit.databases.c_bio_portal_get_gene_info(*, entrez_gene_id, verbose=True)

Parameter	Type	Required / default	Description and constraints
entrez_gene_id	integer	Required	Entrez Gene ID (e.g., 672 for BRCA1)
verbose	bool	True	Progress flag.

Retrieve molecular profiles for a cancer study

dnakit.databases.c_bio_portal_get_molecular_profiles(*, study_id, verbose=True)

Parameter	Type	Required / default	Description and constraints
study_id	string	Required	Cancer study ID
verbose	bool	True	Progress flag.

Retrieve gene mutations from a cancer study

dnakit.databases.c_bio_portal_get_mutations(*, study_id, gene_list, sample_list_id=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
study_id	string	Required	Cancer study ID (e.g., 'brca_tcga')
gene_list	string	Required	Comma-separated gene symbols (e.g., 'BRCA1,BRCA2')
sample_list_id	string	None	Optional sample list ID. If not provided, uses all samples in the study.
verbose	bool	True	Progress flag.

Retrieve samples in a cancer study

dnakit.databases.c_bio_portal_get_samples(*, study_id, page_size=None, page_number=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
study_id	string	Required	Cancer study ID
page_size	integer	None	Maximum number of samples to return. Defaults high enough to return every sample in a study; a smaller value silently truncates the cohort, which will corrupt any frequency denominator computed from it.
page_number	integer	None	0-based page index, used with page_size to page through very large studies.
verbose	bool	True	Progress flag.

Retrieve original CELLxGENE H5AD files

dnakit.databases.cellx_gene_download_h5ad(*, operation=None, dataset_id, output_path=None, census_version=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
operation	string	None	Operation type
dataset_id	string	Required	CELLxGENE dataset identifier (required)
output_path	string	None	Local path to save H5AD file (omit to get URI only)
census_version	string	None	Census version to query. 'stable' (recommended, Long-Term Support release), 'latest' (newest data, may change), or specific date 'YYYY-MM-DD' (for reproducibility). Default 'stable' is best for production analyses.
verbose	bool	True	Progress flag.

Install cellxgene-census before running.

Query filtered single-cell metadata

dnakit.databases.cellx_gene_get_cell_metadata(*, operation=None, organism=None, obs_value_filter=None, column_names=None, census_version=None, gene=None, tissue=None, max_cells=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
operation	string	None	Operation type
organism	string	None	Organism name
obs_value_filter	string	None	REQUIRED - filter cells using SQL-like syntax. Unfiltered queries timeout (50M+ cells). Format: 'field == "value"'. Operators: ==, !=, in, <, >, <=, >=. Combine with 'and'/'or'. Common fields and values: tissue_general (brain, heart, lung, liver, blood, kidney, skin, eye, intestine, pancreas, bone marrow), cell_type (T cell, B cell, neuron, macrophage, fibroblast, epithelial cell, endothelial cell), disease (normal, COVID-19, Alzheimer disease, lung adenocarcinoma), assay (10x 3' v3, Smart-seq2), sex (male, female). Examples: 'tissue_general == "lung"', 'disease == "COVID-19" and tissue_general == "blood"', 'cell_type in ["T cell", "B cell"] and disease == "normal"'.
column_names	array	None	Specific columns to return (default: all columns) {"items": {"type": "string"}}
census_version	string	None	Census version to query. 'stable' (recommended, Long-Term Support release), 'latest' (newest data, may change), or specific date 'YYYY-MM-DD' (for reproducibility). Default 'stable' is best for production analyses.
gene	string	None	Gene identifier or list; follow this operation's identifier conventions and type.
tissue	string	None	Tissue name or identifier understood by the provider.
max_cells	integer	None	Maximum cells returned or processed in this request.
verbose	bool	True	Progress flag.

Install cellxgene-census before running.

Retrieve precomputed cell embeddings

dnakit.databases.cellx_gene_get_embeddings(*, operation=None, organism=None, embedding_name=None, census_version=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
operation	string	None	Operation type
organism	string	None	Organism name
embedding_name	string	None	Name of specific embedding to retrieve (omit to list available embeddings)
census_version	string	None	Census version to query. 'stable' (recommended, Long-Term Support release), 'latest' (newest data, may change), or specific date 'YYYY-MM-DD' (for reproducibility). Default 'stable' is best for production analyses.
verbose	bool	True	Progress flag.

Install cellxgene-census before running.

Query expression data with cell and gene filters

dnakit.databases.cellx_gene_get_expression_data(*, operation=None, organism=None, obs_value_filter=None, var_value_filter=None, obs_column_names=None, var_column_names=None, census_version=None, gene=None, tissue=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
operation	string	None	Operation type
organism	string	None	Organism name
obs_value_filter	string	None	REQUIRED (or use var_value_filter) - Cell filter. Common values: tissue_general (brain, lung, heart, blood, liver), cell_type (T cell, B cell, neuron, macrophage), disease (normal, COVID-19, Alzheimer disease). Example: 'tissue_general == "lung" and disease == "normal"'
var_value_filter	string	None	REQUIRED (or use obs_value_filter) - Gene filter by symbol or Ensembl ID. Examples: 'feature_name in ["TP53", "BRCA1", "EGFR"]', 'feature_name == "CD4"'. Common genes: TP53, EGFR, BRCA1, CD4, CD8A, IL6, TNF, GAPDH.
obs_column_names	array	None	Cell metadata columns to include {"items": {"type": "string"}}
var_column_names	array	None	Gene metadata columns to include {"items": {"type": "string"}}
census_version	string	None	Census version to query. 'stable' (recommended, Long-Term Support release), 'latest' (newest data, may change), or specific date 'YYYY-MM-DD' (for reproducibility). Default 'stable' is best for production analyses.
gene	string	None	Gene identifier or list; follow this operation's identifier conventions and type.
tissue	string	None	Tissue name or identifier understood by the provider.
verbose	bool	True	Progress flag.

Install cellxgene-census before running.

Prepare ChIP-Atlas enrichment submission instructions

dnakit.databases.ch_ipatlas_enrichment_analysis(*, operation=None, bed_data=None, motif=None, gene_list=None, genome=None, antigen_class=None, cell_type_class=None, threshold=None, distance=None, gene=None, cell_type=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
operation	string	None	Provider operation mode; see this row's default and allowed values.
bed_data	string	None	Option 1: BED format genomic regions (tab-separated: chr, start, end). For finding proteins bound to specific genomic regions. Example: 'chr1\t1000\t2000\nchr2\t3000\t4000'.
motif	string	None	Option 2: DNA sequence motif in IUPAC notation. Use: A/T/G/C (bases), W=A|T, S=G|C, M=A|C, K=G|T, R=A|G, Y=C|T, B=C|G|T, D=A|G|T, H=A|C|T, V=A|C|G, N=any. For finding proteins bound to specific DNA sequences. Example: 'CANNTG' (E-box motif).
gene_list	array | string	None	Option 3: Gene symbols (HGNC for human, MGI for mouse, RGD for rat, FlyBase, WormBase, SGD for yeast). Provide as array or single gene. For finding transcription factors regulating genes. Example: ['TP53', 'MDM2', 'CDKN1A']. {"items": {"type": "string"}}
genome	string	None	Genome assembly
antigen_class	string	None	Filter by antigen class (e.g., 'TFs and others', 'Histone', 'RNA polymerase')
cell_type_class	string	None	Filter by cell type class (e.g., 'Blood', 'Liver', 'Brain')
threshold	string	None	Peak calling stringency (MACS2 Q-value). Options: '05'=1e-5 (permissive, more peaks, broader features), '10'=1e-10 (moderate, balanced), '20'=1e-20 (strict, high confidence only, narrow peaks). Default '05' suitable for most analyses. Higher values = fewer but more confident peaks.
distance	string	None	Distance from Transcription Start Site (TSS) in base pairs for gene-TF association. Defines promoter region. Default 5000 (±5kb, captures typical promoters). Use 1000-2000 for narrow promoters, 10000+ for enhancer regions.
gene	array | string	None	DNAKit optional alias for gene_list {"items": {"type": "string"}}
cell_type	string	None	DNAKit optional alias for cell_type_class
verbose	bool	True	Progress flag.

Search ChIP-Atlas experiment metadata

dnakit.databases.ch_ipatlas_get_experiments(*, operation=None, genome=None, antigen=None, cell_type=None, limit=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
operation	string	None	Provider operation mode; see this row's default and allowed values.
genome	string	None	Filter by genome assembly
antigen	string	None	Filter by antigen/protein name (e.g., 'CTCF', 'H3K4me3')
cell_type	string	None	Filter by cell type (e.g., 'K-562', 'HepG2', 'CD4')
limit	integer	None	Maximum results to return
verbose	bool	True	Progress flag.

Retrieve ChIP-Atlas peak resources and local overlaps

dnakit.databases.ch_ipatlas_get_peak_data(*, operation=None, experiment_id=None, genome=None, format=None, threshold=None, gene=None, experiment_type=None, limit=None, peak_file=None, flank_bp=None, max_file_bytes=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
operation	string	None	Provider operation mode; see this row's default and allowed values.
experiment_id	string	None	Experiment ID (SRX/ERX/DRX format, required)
genome	string	None	Genome assembly
format	string	None	Output format
threshold	string	None	Q-value threshold for BED/BigBed peak files. '05'=1e-5 (more peaks), '10'=1e-10 (moderate), '20'=1e-20 (high confidence only). Only applies to BED/BigBed formats. Default '05'.
gene	string	None	Gene identifier or list; follow this operation's identifier conventions and type.
experiment_type	string	None	Experiment type accepted by the source.
limit	integer	None	Maximum results for the current request, not a database-wide total.
peak_file	string	None	Local BED peak file with verified genome assembly and track provenance.
flank_bp	integer	None	Number of flanking bases added on each side of the gene locus.
max_file_bytes	integer	None	Maximum peak-file size in bytes.
verbose	bool	True	Progress flag.

Search ChIP-Atlas datasets by antigen or cell type

dnakit.databases.ch_ipatlas_search_datasets(*, operation=None, antigen=None, cell_type=None, genome=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
operation	string	None	Provider operation mode; see this row's default and allowed values.
antigen	string	None	Search by antigen/protein name (e.g., 'CTCF', 'H3K27ac')
cell_type	string	None	Search by cell type (e.g., 'K-562', 'HeLa', 'MCF-7')
genome	string	None	Genome assembly
verbose	bool	True	Progress flag.

Retrieve gene dependency information from CRISPR screens

dnakit.databases.dep_map_get_gene_dependencies(*, gene_symbol, model_id=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
gene_symbol	string	Required	Gene symbol (e.g., 'EGFR', 'KRAS', 'TP53')
model_id	string	None	Optional: Filter by specific cell line
verbose	bool	True	Progress flag.

Search cancer cell lines by name

dnakit.databases.dep_map_search_cell_lines(*, query, verbose=True)

Parameter	Type	Required / default	Description and constraints
query	string	Required	Search query (cell line name like 'A549', 'MCF7')
verbose	bool	True	Progress flag.

Retrieve variant–expression associations from an eQTL dataset

dnakit.databases.e_qtl_get_associations(*, dataset_id, size=None, gene_id=None, variant=None, molecular_trait_id=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
dataset_id	string	Required	Dataset identifier from eQTL_list_datasets (e.g., 'QTD000001', 'QTD000584')
size	integer	None	Number of associations to return (default 20)
gene_id	string | null	None	Filter by Ensembl gene ID (e.g., 'ENSG00000141510' for TP53). Returns all eQTLs affecting this gene.
variant	string | null	None	Filter by variant in chr_pos_ref_alt format (e.g., 'chr1_791100_G_GGGA'). Returns all genes affected by this variant.
molecular_trait_id	string | null	None	Filter by molecular trait ID (usually same as gene_id for 'ge' datasets)
verbose	bool	True	Progress flag.

List available eQTL study and tissue datasets

dnakit.databases.e_qtl_list_datasets(*, size=None, quant_method=None, tissue_id=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
size	integer	None	Number of datasets to return (default 20)
quant_method	string | null	None	Filter by quantification method: 'ge' (gene expression), 'exon', 'tx' (transcript), 'txrev' (transcript ratio), 'leafcutter' (splicing)
tissue_id	string | null	None	Filter by tissue ontology ID (e.g., 'CL_0000235' for macrophage, 'UBERON_0002107' for liver)
verbose	bool	True	Progress flag.

Retrieve ENCODE biosample metadata

dnakit.databases.encode_get_biosample(*, accession, verbose=True)

Parameter	Type	Required / default	Description and constraints
accession	string	Required	ENCODE biosample accession identifier (format: ENCBS######, e.g., 'ENCBS000AAA', 'ENCBS130ENC'). Find accessions using ENCODE_search_biosamples or from experiment metadata.
verbose	bool	True	Progress flag.

Search chromatin state segmentation annotations

dnakit.databases.encode_get_chromatin_state(*, biosample_term_name=None, organism=None, limit=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
biosample_term_name	string | null	None	Biosample name (e.g., 'K562', 'HepG2', 'GM12878', 'liver'). Leave empty for all.
organism	string	None	Organism scientific name.
limit	integer	None	Maximum number of results.
verbose	bool	True	Progress flag.

Retrieve ENCODE experiment metadata and analysis details

dnakit.databases.encode_get_experiment(*, accession, verbose=True)

Parameter	Type	Required / default	Description and constraints
accession	string	Required	ENCODE experiment accession identifier (format: ENCSR######, e.g., 'ENCSR000AKS', 'ENCSR000CAG'). Find accessions using ENCODE_search_experiments.
verbose	bool	True	Progress flag.

List ENCODE files by format and assay

dnakit.databases.encode_list_files(*, file_type=None, assay_title=None, limit=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
file_type	string	None	File format filter (e.g., 'fastq', 'bam', 'bigWig', 'bed'). Common formats: fastq (raw reads), bam (alignments), bigWig (coverage), bed (peaks/regions).
assay_title	string	None	Assay filter (e.g., 'ChIP-seq', 'RNA-seq'). Filters files by the experimental assay that generated them.
limit	integer	None	Maximum number of results to return (1–100).
verbose	bool	True	Progress flag.

Search cis-regulatory and epigenomic annotations

dnakit.databases.encode_search_annotations(*, annotation_type=None, biosample_term_name=None, organism=None, assembly=None, limit=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
annotation_type	string	None	Annotation type filter. Options: 'candidate Cis-Regulatory Elements' (cCREs), 'chromatin state' (ChromHMM), 'imputed signal' (predicted epigenetic marks). Default: cCREs.
biosample_term_name	string | null	None	Biosample filter (e.g., 'K562', 'HepG2'). Leave empty for all.
organism	string	None	Organism scientific name.
assembly	string	None	Genome assembly (e.g., 'GRCh38', 'hg19', 'mm10').
limit	integer	None	Maximum number of results.
verbose	bool	True	Progress flag.

Search ENCODE biosamples by organism and treatment

dnakit.databases.encode_search_biosamples(*, organism=None, biosample_type=None, treatment=None, limit=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
organism	string	None	Organism filter (e.g., 'Homo sapiens', 'Mus musculus').
biosample_type	string	None	Biosample classification filter — maps to ENCODE's biosample_ontology.classification field (e.g., 'cell line', 'tissue', 'primary cell', 'in vitro differentiated cells').
treatment	string	None	Treatment filter (e.g., 'interferon gamma', 'ethanol'). Use '*' to find any treated samples.
limit	integer	None	Maximum number of results to return (1–100).
verbose	bool	True	Progress flag.

Search ATAC-seq and DNase-seq experiments

dnakit.databases.encode_search_chromatin_accessibility(*, assay_type=None, biosample_term_name=None, organism=None, limit=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
assay_type	string	None	Chromatin accessibility assay: 'ATAC-seq' (Assay for Transposase-Accessible Chromatin, newer/preferred) or 'DNase-seq' (DNase I hypersensitive sites, larger dataset).
biosample_term_name	string | null	None	Biosample name filter (e.g., 'K562', 'GM12878', 'liver'). Leave empty for all.
organism	string	None	Organism scientific name.
limit	integer	None	Maximum number of results to return.
verbose	bool	True	Progress flag.

Search ENCODE experiments through the database module

dnakit.databases.encode_search_experiments(*, assay_title=None, target=None, organism=None, status=None, limit=None, biosample=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
assay_title	string	None	Assay title, for example ATAC-seq.
target	string	None	Assay target or target identifier recognized by the provider.
organism	string	None	Organism name using the provider's naming convention.
status	string	None	Record release or processing status filter.
limit	integer	None	Maximum results for the current request, not a database-wide total.
biosample	string	None	Biosample name or search filter.
verbose	bool	True	Progress flag.

Search histone ChIP-seq experiments by modification

dnakit.databases.encode_search_histone_experiments(*, histone_mark=None, target=None, biosample_term_name=None, biosample=None, organism=None, limit=None, biosample_term=None, cell_type=None, tissue=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
histone_mark	string | null	None	Histone modification mark to filter by (e.g., 'H3K4me3', 'H3K27ac', 'H3K27me3', 'H3K4me1', 'H3K36me3', 'H3K9me3'). Leave empty to search all histone marks.
target	string | null	None	Alias for histone_mark. Histone modification mark (e.g., 'H3K27ac', 'H3K4me3').
biosample_term_name	string | null	None	Biosample name from ENCODE ontology (cell lines or tissues, NOT disease names). Examples: 'K562', 'HepG2', 'GM12878', 'liver', 'brain'. For disease-specific data, search by relevant cell lines (e.g., K562/MOLM-13 for AML). Leave empty to search all.
biosample	string | null	None	Alias for biosample_term_name. Biosample (tissue or cell line, e.g., 'liver', 'K562').
organism	string	None	Organism scientific name (e.g., 'Homo sapiens', 'Mus musculus').
limit	integer	None	Maximum number of results to return (1-100).
biosample_term	string | null	None	Alias for biosample_term_name. Biosample tissue or cell line (e.g., "breast epithelium", "liver", "K562").
cell_type	string | null	None	Alias for biosample_term_name. Cell type or tissue (e.g., 'GM12878', 'K562', 'liver', 'brain').
tissue	string | null	None	Alias for biosample_term_name. Tissue or cell line (e.g., 'liver', 'brain', 'breast epithelium', 'MCF-7').
verbose	bool	True	Progress flag.

Search ENCODE RNA-seq experiments by sample and assay

dnakit.databases.encode_search_rnaseq_experiments(*, biosample_term_name=None, biosample=None, cell_type=None, tissue=None, organism=None, assay_type=None, limit=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
biosample_term_name	string | null	None	Biosample name from ENCODE ontology (e.g., 'K562', 'HepG2', 'GM12878', 'liver', 'brain'). Leave empty to search all biosamples.
biosample	string | null	None	Alias for biosample_term_name. Cell type or tissue (e.g., 'K562', 'liver').
cell_type	string | null	None	Alias for biosample_term_name. Cell type (e.g., 'K562', 'HepG2', 'GM12878').
tissue	string | null	None	Alias for biosample_term_name. Tissue type (e.g., 'liver', 'brain', 'heart').
organism	string	None	Organism scientific name (e.g., 'Homo sapiens', 'Mus musculus').
assay_type	string	None	RNA-seq assay type: 'total RNA-seq' (default, all RNA), 'polyA plus RNA-seq' (mRNA), 'small RNA-seq', 'microRNA-seq'. Aliases: 'total', 'polya', 'mirna', 'small'.
limit	integer	None	Maximum number of results to return (1-100).
verbose	bool	True	Progress flag.

Search differential expression experiment records

dnakit.databases.expression_atlas_search_differential(*, gene=None, condition=None, species=None, limit=None, offset=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
gene	string	None	Gene symbol or Ensembl ID (e.g., 'TP53', 'ENSG00000141510')
condition	string	None	Condition/disease to filter by (e.g., 'cancer', 'inflammation', 'breast')
species	string	None	Species name (default: 'homo sapiens')
limit	integer | null	None	Maximum number of experiments to return (default 50, max 500). Compare with the total reported in the response to see how many exist.
offset	integer | null	None	Zero-based index of the first experiment to return, for paging through results beyond the first page (e.g. offset=50 returns 51-100). Default: 0.
verbose	bool	True	Progress flag.

Search baseline and differential expression experiments

dnakit.databases.expression_atlas_search_experiments(*, gene=None, condition=None, species=None, limit=None, offset=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
gene	string	None	Gene symbol or Ensembl ID
condition	string	None	Biological condition or tissue (e.g., 'brain', 'cancer', 'kidney')
species	string	None	Species name (optional, e.g., 'homo sapiens')
limit	integer | null	None	Maximum number of experiments to return (default 50, max 500). Compare with the total reported in the response to see how many exist.
offset	integer | null	None	Zero-based index of the first experiment to return, for paging through results beyond the first page (e.g. offset=50 returns 51-100). Default: 0.
verbose	bool	True	Progress flag.

Search Hi-C and chromatin conformation data

dnakit.databases.four_dn_search_data(*, operation=None, query=None, item_type=None, file_type=None, assay_title=None, biosource_name=None, limit=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
operation	string	None	Provider operation mode; see this row's default and allowed values.
query	string	None	Search query (default: '' for all) {"default": ""}
item_type	string	None	Type of item to search
file_type	string	None	Filter by file type. Common types: 'contact list' (processed contact matrices), 'pairs' (aligned read pairs), 'cooler' (multi-resolution contact matrices), 'mcool' (multi-resolution cooler), 'hic' (Juicer format).
assay_title	string	None	Filter by assay (e.g., 'Hi-C', 'Micro-C', 'Capture Hi-C')
biosource_name	string	None	Filter by cell type (e.g., 'H1-hESC', 'HFFc6', 'GM12878')
limit	integer	None	Maximum results to return
verbose	bool	True	Progress flag.

Retrieve GDC cancer case clinical data

dnakit.databases.gdc_get_clinical_data(*, project_id=None, primary_site=None, disease_type=None, vital_status=None, gender=None, size=None, offset=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
project_id	string	None	GDC project identifier (e.g., 'TCGA-BRCA', 'TCGA-LUAD', 'TARGET-AML')
primary_site	string	None	Primary anatomical site (e.g., 'Breast', 'Lung', 'Brain')
disease_type	string	None	Disease type filter (e.g., 'Ductal and Lobular Neoplasms')
vital_status	string	None	Vital status filter: 'Alive' or 'Dead'
gender	string	None	Gender filter: 'female' or 'male'
size	integer	None	Number of cases to return (1-100)
offset	integer	None	Pagination offset (0-based)
verbose	bool	True	Progress flag.

Retrieve pan-cancer gene mutation frequencies

dnakit.databases.gdc_get_mutation_frequency(*, gene_symbol=None, gene=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
gene_symbol	string	None	Gene symbol (e.g., 'TP53', 'KRAS')
gene	string	None	Gene symbol alias — alternative to gene_symbol
verbose	bool	True	Progress flag.

Retrieve GDC somatic mutations by gene

dnakit.databases.gdc_get_ssm_by_gene(*, gene_symbol, project_id=None, size=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
gene_symbol	string	Required	Gene symbol (e.g., 'TP53', 'EGFR', 'BRAF')
project_id	string	None	Optional: Filter by project (e.g., 'TCGA-BRCA')
size	integer	None	Number of results (1–100)
verbose	bool	True	Progress flag.

Retrieve cancer cohort survival and censoring data

dnakit.databases.gdc_get_survival(*, project_id, gene_symbol=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
project_id	string	Required	GDC project identifier (e.g., 'TCGA-BRCA', 'TCGA-LUAD', 'TCGA-GBM')
gene_symbol	string	None	Optional: gene symbol to filter cases with mutations in this gene (e.g., 'TP53', 'KRAS')
verbose	bool	True	Progress flag.

List GDC files by data type

dnakit.databases.gdc_list_files(*, data_type=None, size=None, offset=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
data_type	string	None	Data type filter (e.g., 'Gene Expression Quantification')
size	integer	None	Number of results (1–100)
offset	integer	None	Offset for pagination (0-based)
verbose	bool	True	Progress flag.

List GDC cancer projects and summaries

dnakit.databases.gdc_list_projects(*, program=None, size=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
program	string	None	Filter by program (e.g., 'TCGA', 'TARGET')
size	integer	None	Number of results (1–100)
verbose	bool	True	Progress flag.

Search GDC cancer cases with filters

dnakit.databases.gdc_search_cases(*, project_id=None, size=None, offset=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
project_id	string	None	GDC project identifier (e.g., 'TCGA-BRCA')
size	integer	None	Number of results (1–100)
offset	integer	None	Offset for pagination (0-based)
verbose	bool	True	Progress flag.

Search GEO ATAC-seq datasets

dnakit.databases.geo_search_atacseq_datasets(*, query=None, organism=None, limit=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
query	string | null	None	Search query (e.g., 'T cell differentiation', 'liver hepatocyte', 'hematopoiesis'). Leave empty to search broadly.
organism	string	None	Organism scientific name (e.g., 'Homo sapiens', 'Mus musculus').
limit	integer	None	Maximum number of results to return (1-100).
verbose	bool	True	Progress flag.

Search GEO ChIP-seq datasets

dnakit.databases.geo_search_chipseq_datasets(*, query, organism=None, limit=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
query	string	Required	Search terms for ChIP-seq datasets (e.g., 'H3K27ac liver', 'CTCF cancer', 'p53 ChIP-seq').
organism	string	None	Organism filter.
limit	integer	None	Maximum number of dataset IDs to return.
verbose	bool	True	Progress flag.

Search GEO RNA-seq datasets

dnakit.databases.geo_search_rnaseq_datasets(*, query=None, organism=None, limit=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
query	string | null	None	Search query (e.g., 'BRCA1 breast cancer', 'T cell activation', 'Alzheimer disease'). Leave empty to search broadly.
organism	string	None	Organism scientific name (e.g., 'Homo sapiens', 'Mus musculus').
limit	integer	None	Maximum number of results to return (1-100).
verbose	bool	True	Progress flag.

Calculate a gene–variant eQTL association in a tissue

dnakit.databases.gtex_calculate_eqtl(*, operation=None, gencode_id, variant_id, tissue_site_detail_id, dataset_id=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
operation	string	None	Operation type
gencode_id	string	Required	Required: Versioned GENCODE ID (e.g. ENSG00000141510.18)
variant_id	string	Required	Required: GTEx variant ID
tissue_site_detail_id	string	Required	Required: Tissue ID (e.g. 'Whole_Blood')
dataset_id	string	None	Provider dataset identifier.
verbose	bool	True	Progress flag.

Retrieve GTEx gene expression summaries

dnakit.databases.gtex_get_expression_summary(*, gene_symbol=None, ensembl_gene_id=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
gene_symbol	string	None	Gene symbol (e.g., TP53, BRCA1). Auto-resolved to GENCODE ID.
ensembl_gene_id	string	None	Ensembl gene ID, e.g., ENSG00000141510
verbose	bool	True	Progress flag.

Retrieve median gene expression across tissues

dnakit.databases.gtex_get_median_gene_expression(*, operation=None, gencode_id=None, tissue_site_detail_id=None, dataset_id=None, page=None, items_per_page=None, gene_symbol=None, gene=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
operation	string	None	Operation type
gencode_id	string | array	None	Gene identifier(s): gene symbol (e.g. 'TP53'), unversioned Ensembl ID (e.g. 'ENSG00000141510'), or versioned GENCODE ID (e.g. 'ENSG00000141510.18'). Auto-resolved to versioned GENCODE ID. Can be single string or array. {"items": {"type": "string"}}
tissue_site_detail_id	array	None	Optional: Tissue IDs to filter (e.g. ['Liver', 'Brain_Cortex']). Omit for all tissues. See GTEx_get_tissue_sites for valid IDs {"items": {"type": "string"}}
dataset_id	string	None	GTEx dataset version (default: gtex_v8, the most widely cited release). gtex_v10 is the newer release (943 eQTL donors vs 838) and is fully queryable -- gene IDs are resolved to each dataset's own GENCODE version automatically.
page	integer	None	Page number for pagination (0-based)
items_per_page	integer	None	Results per page
gene_symbol	string	None	Gene symbol alias for gencode_id (e.g., "TP53", "COL5A1")
gene	string	None	DNAKit optional alias for gene_symbol
verbose	bool	True	Progress flag.

Retrieve multi-tissue eQTL meta-analysis results

dnakit.databases.gtex_get_multi_tissue_eqtls(*, operation=None, gencode_id, variant_id=None, dataset_id=None, page=None, items_per_page=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
operation	string	None	Operation type
gencode_id	string	Required	Required: Versioned GENCODE ID
variant_id	string	None	Optional: GTEx variant ID to filter specific variant
dataset_id	string	None	Provider dataset identifier.
page	integer	None	Result page number; the starting page convention follows the provider.
items_per_page	integer	None	Number of records requested per page.
verbose	bool	True	Progress flag.

Retrieve significant single-tissue eQTL associations

dnakit.databases.gtex_get_single_tissue_eqtls(*, operation=None, gencode_id=None, variant_id=None, tissue_site_detail_id=None, dataset_id=None, page=None, items_per_page=None, gene_symbol=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
operation	string	None	Operation type
gencode_id	array	None	Optional: Versioned GENCODE ID(s) to query {"items": {"type": "string"}}
variant_id	array	None	Optional: GTEx variant ID(s) to query {"items": {"type": "string"}}
tissue_site_detail_id	array	None	Optional: Tissue ID(s) to filter. At least one of gencode_id, variant_id, or tissue_site_detail_id required {"items": {"type": "string"}}
dataset_id	string	None	Provider dataset identifier.
page	integer	None	Result page number; the starting page convention follows the provider.
items_per_page	integer	None	Number of records requested per page.
gene_symbol	string	None	Gene symbol, for example BRCA1.
verbose	bool	True	Progress flag.

List GTEx tissue sites and sample statistics

dnakit.databases.gtex_get_tissue_sites(*, operation=None, dataset_id=None, page=None, items_per_page=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
operation	string	None	Operation type
dataset_id	string	None	GTEx dataset version
page	integer	None	Page number
items_per_page	integer	None	Results per page
verbose	bool	True	Progress flag.

Query GTEx single-tissue eQTL data

dnakit.databases.gtex_query_eqtl(*, gene_symbol=None, ensembl_gene_id=None, page=None, size=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
gene_symbol	string	None	Gene symbol (e.g., TP53, BRCA1). Auto-resolved to GENCODE ID.
ensembl_gene_id	string	None	Ensembl gene ID, e.g., ENSG00000141510
page	integer	None	Page number (1-based)
size	integer	None	Page size (1–100)
verbose	bool	True	Progress flag.

Aggregate gene information across genomics datasets

dnakit.databases.harmonizome_get_gene(*, gene_symbol, verbose=True)

Parameter	Type	Required / default	Description and constraints
gene_symbol	string	Required	Official gene symbol (case-insensitive). Examples: 'TP53', 'BRCA1', 'EGFR', 'KRAS', 'CDK2'.
verbose	bool	True	Progress flag.

Retrieve associations between gene expression and cancer survival

dnakit.databases.hpa_get_cancer_prognostics_by_gene(*, ensembl_id=None, gene_name=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
ensembl_id	string	None	Ensembl Gene ID of the gene to check, e.g., 'ENSG00000141510' for TP53, 'ENSG00000012048' for BRCA1.
gene_name	string	None	DNAKit optional alias for ensembl_id
verbose	bool	True	Progress flag.

Inspect the retired HPA protein interaction query

dnakit.databases.hpa_get_protein_interactions_by_gene(*, gene_name, verbose=True)

Parameter	Type	Required / default	Description and constraints
gene_name	string	Required	Official gene symbol, e.g., 'EGFR', 'TP53', 'BRCA1', etc.
verbose	bool	True	Progress flag.

Retrieve RNA expression by biological source

dnakit.databases.hpa_get_rna_expression_by_source(*, gene_name, source_type, source_name, verbose=True)

Parameter	Type	Required / default	Description and constraints
gene_name	string	Required	Gene name or gene symbol, e.g., 'GFAP', 'TP53', 'BRCA1', etc.
source_type	string	Required	The type of biological source. Choose from: 'tissue' (51 consensus tissues, nTPM), 'blood' (19 immune cell subsets, nTPM), 'brain' (13 brain regions, nTPM), 'single_cell' (~160 single cell types, nCPM).
source_name	string	Required	The specific source name, e.g. 'liver', 'heart_muscle', 'skin', 't_cell', 'hepatocyte', 'cerebellum'. Case-insensitive; spaces and hyphens are treated as underscores. Names HPA publishes only as subsets (blood 't_cell', 'b_cell', 'monocyte', 'dendritic_cell') resolve to a representative subset column and the response reports which one in a 'note'. An invalid name returns an error listing valid names -- it never returns a silent 'N/A'.
verbose	bool	True	Progress flag.

Retrieve gene RNA expression in selected tissues

dnakit.databases.hpa_get_rna_expression_in_specific_tissues(*, ensembl_id=None, tissue_names=None, tissues=None, gene_name=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
ensembl_id	string	None	Ensembl Gene ID for the gene, e.g., 'ENSG00000141510' for TP53.
tissue_names	array	None	List of tissue names to query, e.g., ['skin', 'liver', 'heart muscle', 'kidney']. Case-insensitive; underscores, spaces and hyphens are interchangeable. HPA has no RNA column for 'bronchus', 'nasopharynx', 'oral mucosa' or 'soft tissue' (protein/IHC only). {"items": {"type": "string"}}
tissues	array	None	DNAKit optional alias for tissue_names {"items": {"type": "string"}}
gene_name	string	None	DNAKit optional alias for ensembl_id
verbose	bool	True	Progress flag.

Retrieve protein subcellular localization annotations

dnakit.databases.hpa_get_subcellular_location(*, gene_name, verbose=True)

Parameter	Type	Required / default	Description and constraints
gene_name	string	Required	Gene name or gene symbol, e.g., 'CCNB1', 'TP53', 'EGFR', etc.
verbose	bool	True	Progress flag.

Search HPA genes and Ensembl identifiers

dnakit.databases.hpa_search_genes_by_query(*, search_query, max_results=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
search_query	string	Required	Gene name, alias, keyword, or cell line name to search for, e.g., 'EGFR', 'TP53', or 'MCF7'.
max_results	integer | null	None	Maximum number of gene matches to return (default: 50). This search does a broad full-text match with no server-side limit, so a short/common query can otherwise return thousands of results; exact gene-symbol matches are ranked first.
verbose	bool	True	Progress flag.

Retrieve transcription factor binding matrices and metadata

dnakit.databases.jaspar_get_matrix(*, matrix_id, verbose=True)

Parameter	Type	Required / default	Description and constraints
matrix_id	string	Required	JASPAR matrix ID (e.g., 'MA0002.2'). You can discover IDs with JASPAR_get_transcription_factors.
verbose	bool	True	Progress flag.

List available versions of a JASPAR matrix

dnakit.databases.jaspar_get_matrix_versions(*, base_id, page=None, page_size=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
base_id	string	Required	JASPAR base matrix ID without version (e.g., 'MA0002'). You can get base_id from jaspar_get_matrix.
page	integer	None	Page number (1-based).
page_size	integer	None	Results per page.
verbose	bool	True	Progress flag.

Browse JASPAR transcription factor binding profiles

dnakit.databases.jaspar_get_transcription_factors(*, collection=None, page=None, page_size=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
collection	string	None	JASPAR collection (e.g., CORE).
page	integer	None	Page number (1-based).
page_size	integer	None	Results per page (JASPAR page_size).
verbose	bool	True	Progress flag.

Search binding matrices by name, species or taxonomic group

dnakit.databases.jaspar_search_matrices(*, search=None, name=None, collection=None, tax_group=None, species=None, page=None, page_size=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
search	string	None	Free-text search across matrices (e.g., 'CTCF').
name	string	None	Filter by TF name (e.g., 'CTCF').
collection	string	None	Filter by collection (e.g., 'CORE').
tax_group	string	None	Filter by taxonomic group (e.g., 'vertebrates').
species	string	None	Filter by NCBI taxonomy ID (e.g., '9606' for human). Sent to JASPAR as its tax_id query parameter.
page	integer	None	Page number (1-based).
page_size	integer	None	Results per page.
verbose	bool	True	Progress flag.

Retrieve transcription factor binding sites by gene and cell type

dnakit.databases.re_map_get_transcription_factor_binding(*, gene_name, cell_type=None, limit=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
gene_name	string	Required	Gene symbol (e.g., BRCA1, TP53, MYC)
cell_type	string	None	Cell type (e.g., HepG2, K562, MCF-7)
limit	integer	None	Number of results to return
verbose	bool	True	Progress flag.

Retrieve regulatory variant annotations by rsID

dnakit.databases.regulome_db_query_variant(*, rsid=None, variant=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
rsid	string	None	dbSNP rsID (e.g., 'rs4994', 'rs429358')
variant	string	None	Alias for rsid. dbSNP rsID (e.g., 'rs7903146', 'rs429358').
verbose	bool	True	Progress flag.

Retrieve candidate cis-regulatory elements in an interval

dnakit.databases.screen_get_regulatory_elements(*, gene_name=None, query=None, element_type=None, limit=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
gene_name	string	None	Gene symbol to search for regulatory elements (e.g., BRCA1, TP53). Alias: 'query'.
query	string	None	Gene symbol to search for regulatory elements (alias for gene_name).
element_type	string	None	Type of regulatory element (promoter, enhancer, insulator)
limit	integer	None	Number of results to return
verbose	bool	True	Progress flag.

Retrieve ENCODE candidate cis-regulatory elements from UCSC

dnakit.databases.ucsc_get_encode_c_cres(*, genome=None, chrom, start, end, verbose=True)

Parameter	Type	Required / default	Description and constraints
genome	string	None	Genome assembly (e.g., 'hg38', 'mm10').
chrom	string	Required	Chromosome name (e.g., 'chr17').
start	integer	Required	Start position (0-based).
end	integer	Required	End position (0-based).
verbose	bool	True	Progress flag.

Retrieve a direct transcription factor binding dataset

dnakit.databases.uni_bind_get_dataset(*, operation=None, dataset_id, verbose=True)

Parameter	Type	Required / default	Description and constraints
operation	string	None	Operation selector. Must be 'get_dataset'.
dataset_id	string	Required	UniBind dataset identifier, e.g. 'EXP030726.neural_stem_cells.SMAD3'. Obtain from UniBind_search_datasets (the 'dataset_id' field).
verbose	bool	True	Progress flag.

List transcription factors in UniBind

dnakit.databases.uni_bind_list_tfs(*, operation=None, search=None, limit=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
operation	string	None	Operation selector. Must be 'list_tfs'.
search	string | null	None	Case-insensitive substring filter applied client-side to TF gene symbols, e.g. 'SMAD', 'FOX', 'GATA'. Optional; omit to list all TFs.
limit	integer	None	Maximum number of TF names to return after filtering.
verbose	bool	True	Progress flag.

Search binding datasets by transcription factor and cell context

dnakit.databases.uni_bind_search_datasets(*, operation=None, tf_name=None, species=None, cell_line=None, collection=None, order=None, page=None, page_size=None, verbose=True)

Parameter	Type	Required / default	Description and constraints
operation	string	None	Operation selector. Must be 'search_datasets'.
tf_name	string | null	None	Transcription factor gene symbol to filter by, e.g. 'CTCF', 'SMAD3', 'ESR1'. Exact match on UniBind's TF name. Optional.
species	string | null	None	Species scientific name to filter by, e.g. 'Homo sapiens', 'Mus musculus', 'Drosophila melanogaster'. Optional.
cell_line	string | null	None	Cell type / tissue / condition name to filter by, e.g. 'neural stem cells', 'MCF7'. Optional.
collection	string | null	None	UniBind collection: 'Robust' (high-confidence, metadata-curated) or 'Permissive' (broader). Optional.
order	string | null	None	Field to order results by, e.g. 'tf_name' or '-tf_name' (prefix '-' for descending). Optional.
page	integer	None	1-based page number for pagination.
page_size	integer	None	Number of datasets per page (max 1000).
verbose	bool	True	Progress flag.