表达、调控与肿瘤数据查询：参数与补充说明

用法和示例见功能教程。

各功能按作用、API、输入、输出、示例代码和结果说明介绍。运行前按说明准备凭据、本地文件与可选依赖；远程结果随数据库版本与查询时间变化。

ChIP-Atlas 按 gene 查峰时，未提供 peak_file 会返回 requires_data 和检索计划；提供已核对组装的 BED 后才计算区间重叠。富集入口返回 requires_submission 提交说明，不能把它当成已计算的富集统计。

分页查询 cBioPortal 肿瘤研究目录

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

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。

按 Entrez 编号查询肿瘤数据库基因信息

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

参数	类型	必填 / 默认值	说明与约束
entrez_gene_id	integer	必填	Entrez Gene ID (e.g., 672 for BRCA1)
verbose	bool	True	运行提示开关。

查询肿瘤研究的分子数据类型

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

参数	类型	必填 / 默认值	说明与约束
study_id	string	必填	Cancer study ID
verbose	bool	True	运行提示开关。

查询肿瘤研究中指定基因的突变

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

参数	类型	必填 / 默认值	说明与约束
study_id	string	必填	Cancer study ID (e.g., 'brca_tcga')
gene_list	string	必填	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	运行提示开关。

查询肿瘤研究的样本集合

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

参数	类型	必填 / 默认值	说明与约束
study_id	string	必填	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	运行提示开关。

获取 CELLxGENE 原始 H5AD 数据文件

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

参数	类型	必填 / 默认值	说明与约束
operation	string	None	Operation type
dataset_id	string	必填	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	运行提示开关。

运行前安装 cellxgene-census。

按筛选条件查询单细胞元数据

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)

参数	类型	必填 / 默认值	说明与约束
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	基因标识或基因列表；命名要求和类型见当前接口。
tissue	string	None	目标组织名称或标识，按当前数据源填写。
max_cells	integer	None	本次返回或处理的细胞数上限。
verbose	bool	True	运行提示开关。

运行前安装 cellxgene-census。

获取预计算的单细胞嵌入表示

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

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。

运行前安装 cellxgene-census。

按细胞与基因条件查询表达矩阵

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)

参数	类型	必填 / 默认值	说明与约束
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	基因标识或基因列表；命名要求和类型见当前接口。
tissue	string	None	目标组织名称或标识，按当前数据源填写。
verbose	bool	True	运行提示开关。

运行前安装 cellxgene-census。

生成 ChIP-Atlas 富集任务提交说明

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)

参数	类型	必填 / 默认值	说明与约束
operation	string	None	提供方操作模式；默认值与允许值见本行约束。
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	运行提示开关。

检索 ChIP-Atlas 实验元数据

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

参数	类型	必填 / 默认值	说明与约束
operation	string	None	提供方操作模式；默认值与允许值见本行约束。
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	运行提示开关。

查询 ChIP-Atlas 峰资源与本地区间重叠

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)

参数	类型	必填 / 默认值	说明与约束
operation	string	None	提供方操作模式；默认值与允许值见本行约束。
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	基因标识或基因列表；命名要求和类型见当前接口。
experiment_type	string	None	实验类别，按数据源接受的类型筛选。
limit	integer	None	当前请求的返回数量上限；不是全库命中总数。
peak_file	string	None	本地 BED 峰文件；必须核对其基因组版本和轨道来源。
flank_bp	integer	None	基因区域两侧扩展的碱基数。
max_file_bytes	integer	None	允许读取的峰文件字节上限。
verbose	bool	True	运行提示开关。

按抗原或细胞类型检索 ChIP-Atlas 数据集

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

参数	类型	必填 / 默认值	说明与约束
operation	string	None	提供方操作模式；默认值与允许值见本行约束。
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	运行提示开关。

查询 CRISPR 筛选的基因依赖信息

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

参数	类型	必填 / 默认值	说明与约束
gene_symbol	string	必填	Gene symbol (e.g., 'EGFR', 'KRAS', 'TP53')
model_id	string	None	Optional: Filter by specific cell line
verbose	bool	True	运行提示开关。

按名称检索肿瘤细胞系

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

参数	类型	必填 / 默认值	说明与约束
query	string	必填	Search query (cell line name like 'A549', 'MCF7')
verbose	bool	True	运行提示开关。

查询 eQTL 数据集中的变异表达关联

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

参数	类型	必填 / 默认值	说明与约束
dataset_id	string	必填	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	运行提示开关。

列出可用的 eQTL 研究与组织数据集

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

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。

查询 ENCODE 生物样本完整元数据

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

参数	类型	必填 / 默认值	说明与约束
accession	string	必填	ENCODE biosample accession identifier (format: ENCBS######, e.g., 'ENCBS000AAA', 'ENCBS130ENC'). Find accessions using ENCODE_search_biosamples or from experiment metadata.
verbose	bool	True	运行提示开关。

检索染色质状态分割注释

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

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。

查询 ENCODE 实验元数据与分析信息

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

参数	类型	必填 / 默认值	说明与约束
accession	string	必填	ENCODE experiment accession identifier (format: ENCSR######, e.g., 'ENCSR000AKS', 'ENCSR000CAG'). Find accessions using ENCODE_search_experiments.
verbose	bool	True	运行提示开关。

按格式与实验类型列出 ENCODE 文件

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

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。

检索顺式调控元件与表观组注释

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

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。

按物种与处理条件检索 ENCODE 样本

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

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。

检索 ATAC-seq 与 DNase-seq 实验

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

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。

通过数据库模块检索 ENCODE 实验

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

参数	类型	必填 / 默认值	说明与约束
assay_title	string	None	实验方法名称，例如 ATAC-seq。
target	string	None	实验靶标或目标标识，按当前数据源填写。
organism	string	None	目标生物名称，按提供方命名规则填写。
status	string	None	记录的发布或处理状态筛选条件。
limit	integer	None	当前请求的返回数量上限；不是全库命中总数。
biosample	string	None	生物样本名称或检索条件。
verbose	bool	True	运行提示开关。

按组蛋白修饰检索 ChIP-seq 实验

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)

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。

按样本与实验类型检索 ENCODE RNA-seq

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)

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。

检索差异表达实验的项目记录

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

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。

检索基线与差异表达实验

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

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。

检索 Hi-C 与染色质构象数据

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)

参数	类型	必填 / 默认值	说明与约束
operation	string	None	提供方操作模式；默认值与允许值见本行约束。
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	运行提示开关。

查询 GDC 肿瘤病例的临床资料

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)

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。

查询基因在泛癌队列中的突变频率

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

参数	类型	必填 / 默认值	说明与约束
gene_symbol	string	None	Gene symbol (e.g., 'TP53', 'KRAS')
gene	string	None	Gene symbol alias — alternative to gene_symbol
verbose	bool	True	运行提示开关。

按基因查询 GDC 体细胞突变

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

参数	类型	必填 / 默认值	说明与约束
gene_symbol	string	必填	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	运行提示开关。

查询肿瘤队列的生存与删失数据

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

参数	类型	必填 / 默认值	说明与约束
project_id	string	必填	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	运行提示开关。

按数据类型列出 GDC 文件

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

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。

列出 GDC 肿瘤项目与汇总信息

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

参数	类型	必填 / 默认值	说明与约束
program	string	None	Filter by program (e.g., 'TCGA', 'TARGET')
size	integer	None	Number of results (1–100)
verbose	bool	True	运行提示开关。

按筛选条件检索 GDC 肿瘤病例

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

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。

检索 GEO 染色质可及性数据集

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

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。

检索 GEO 蛋白质 DNA 结合数据集

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

参数	类型	必填 / 默认值	说明与约束
query	string	必填	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	运行提示开关。

检索 GEO 转录组表达数据集

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

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。

计算指定组织中基因与变异的 eQTL 关联

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

参数	类型	必填 / 默认值	说明与约束
operation	string	None	Operation type
gencode_id	string	必填	Required: Versioned GENCODE ID (e.g. ENSG00000141510.18)
variant_id	string	必填	Required: GTEx variant ID
tissue_site_detail_id	string	必填	Required: Tissue ID (e.g. 'Whole_Blood')
dataset_id	string	None	提供方的数据集标识。
verbose	bool	True	运行提示开关。

查询基因的 GTEx 表达摘要

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

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。

查询基因在不同组织中的表达中位数

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)

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。

查询跨组织 eQTL 荟萃分析结果

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)

参数	类型	必填 / 默认值	说明与约束
operation	string	None	Operation type
gencode_id	string	必填	Required: Versioned GENCODE ID
variant_id	string	None	Optional: GTEx variant ID to filter specific variant
dataset_id	string	None	提供方的数据集标识。
page	integer	None	结果页码；起始页约定按提供方参数说明。
items_per_page	integer	None	每页返回的记录数。
verbose	bool	True	运行提示开关。

查询显著的单组织 eQTL 关联

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)

参数	类型	必填 / 默认值	说明与约束
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	提供方的数据集标识。
page	integer	None	结果页码；起始页约定按提供方参数说明。
items_per_page	integer	None	每页返回的记录数。
gene_symbol	string	None	基因符号，例如 BRCA1。
verbose	bool	True	运行提示开关。

列出 GTEx 组织类型与样本统计

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

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。

按条件查询 GTEx 单组织 eQTL

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

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。

汇总多组学数据中的基因信息

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

参数	类型	必填 / 默认值	说明与约束
gene_symbol	string	必填	Official gene symbol (case-insensitive). Examples: 'TP53', 'BRCA1', 'EGFR', 'KRAS', 'CDK2'.
verbose	bool	True	运行提示开关。

查询基因表达与肿瘤生存的关联

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

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。

查看已停用的 HPA 蛋白互作查询

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

参数	类型	必填 / 默认值	说明与约束
gene_name	string	必填	Official gene symbol, e.g., 'EGFR', 'TP53', 'BRCA1', etc.
verbose	bool	True	运行提示开关。

按组织或细胞来源查询 RNA 表达

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

参数	类型	必填 / 默认值	说明与约束
gene_name	string	必填	Gene name or gene symbol, e.g., 'GFAP', 'TP53', 'BRCA1', etc.
source_type	string	必填	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	必填	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	运行提示开关。

查询基因在指定组织中的 RNA 表达

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

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。

查询蛋白质亚细胞定位注释

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

参数	类型	必填 / 默认值	说明与约束
gene_name	string	必填	Gene name or gene symbol, e.g., 'CCNB1', 'TP53', 'EGFR', etc.
verbose	bool	True	运行提示开关。

检索 HPA 基因与 Ensembl 标识

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

参数	类型	必填 / 默认值	说明与约束
search_query	string	必填	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	运行提示开关。

获取转录因子结合矩阵与元数据

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

参数	类型	必填 / 默认值	说明与约束
matrix_id	string	必填	JASPAR matrix ID (e.g., 'MA0002.2'). You can discover IDs with JASPAR_get_transcription_factors.
verbose	bool	True	运行提示开关。

列出 JASPAR 结合矩阵的历史版本

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

参数	类型	必填 / 默认值	说明与约束
base_id	string	必填	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	运行提示开关。

分页列出 JASPAR 转录因子结合谱

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

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。

按名称、物种或分类检索结合矩阵

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

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。

查询基因与细胞类型对应的转录因子结合位点

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

参数	类型	必填 / 默认值	说明与约束
gene_name	string	必填	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	运行提示开关。

按 rsID 查询变异调控注释

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

参数	类型	必填 / 默认值	说明与约束
rsid	string	None	dbSNP rsID (e.g., 'rs4994', 'rs429358')
variant	string	None	Alias for rsid. dbSNP rsID (e.g., 'rs7903146', 'rs429358').
verbose	bool	True	运行提示开关。

查询基因组区间的候选顺式调控元件

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

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。

从 UCSC 获取 ENCODE 候选顺式调控元件

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

参数	类型	必填 / 默认值	说明与约束
genome	string	None	Genome assembly (e.g., 'hg38', 'mm10').
chrom	string	必填	Chromosome name (e.g., 'chr17').
start	integer	必填	Start position (0-based).
end	integer	必填	End position (0-based).
verbose	bool	True	运行提示开关。

查询单个直接转录因子结合数据集

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

参数	类型	必填 / 默认值	说明与约束
operation	string	None	Operation selector. Must be 'get_dataset'.
dataset_id	string	必填	UniBind dataset identifier, e.g. 'EXP030726.neural_stem_cells.SMAD3'. Obtain from UniBind_search_datasets (the 'dataset_id' field).
verbose	bool	True	运行提示开关。

列出 UniBind 收录的转录因子

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

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。

按转录因子与细胞条件检索结合数据集

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)

参数	类型	必填 / 默认值	说明与约束
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	运行提示开关。