基因集与通路富集：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。

对基因集合执行指定库的富集分析¶

dnakit.databases.enrichr_enrich(*, operation=None, gene_list, library=None, top_n=None, species=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`operation`	string	None	Operation type (fixed: enrich)
`gene_list`	array	必填	List of gene symbols (e.g., ['TP53', 'BRCA1', 'EGFR']). Minimum 1 gene. {"items": {"type": "string"}}
`library`	string	None	Enrichr library name (default: GO_Biological_Process_2023). Common: GO_Biological_Process_2023, KEGG_2021_Human, Reactome_2022, WikiPathways_2024_Human, MSigDB_Hallmark_2020
`top_n`	integer	None	Number of top enriched terms to return (default: 10)
`species`	string \| null	None	Organism instance to query: 'human' (default), 'mouse', 'fly' (FlyEnrichr), 'worm' (WormEnrichr), 'yeast' (YeastEnrichr), or 'fish' (FishEnrichr). Gene set libraries differ per organism, and gene symbols must match that organism's nomenclature.
`verbose`	bool	True	运行提示开关。

dnakit.databases.enrichr_gene_enrichment_analysis(*, gene_list, libs=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`gene_list`	array	必填	List of gene names or symbols to analyze. At least 2 genes are required for path ranking analysis. {"items": {"type": "string"}, "minItems": 2}
`libs`	array	None	List of Enrichr enrichment libraries to query (e.g. 'KEGG_2021_Human', 'GO_Biological_Process_2023'). Omitting this or passing an empty list uses a broad default set of pathway/ontology libraries. {"items": {"type": "string"}, "default": ["WikiPathways_2024_Human", "Reactome_Pathways_2024", "MSigDB_Hallmark_2020", "GO_Molecular_Function_2023", "GO_Biological_Process_2023"]}
`verbose`	bool	True	运行提示开关。

dnakit.databases.panther_enrichment(*, gene_list, organism=None, annotation_dataset=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`gene_list`	string	必填	Comma-separated list of gene symbols, UniProt IDs, or Ensembl IDs. Example: 'TP53,BRCA1,EGFR,KRAS,PTEN,APC,RB1'.
`organism`	integer \| null	None	NCBI taxonomy ID. Default: 9606 (human). Others: 10090 (mouse), 7227 (fly), 559292 (yeast).
`annotation_dataset`	string \| null	None	Annotation dataset for enrichment. Options: 'GO:0008150' (biological_process, default), 'GO:0003674' (molecular_function), 'GO:0005575' (cellular_component), 'ANNOT_TYPE_ID_PANTHER_PATHWAY' (PANTHER pathway), 'ANNOT_TYPE_ID_REACTOME_PATHWAY' (Reactome pathway), 'ANNOT_TYPE_ID_PANTHER_PC' (protein class).
`verbose`	bool	True	运行提示开关。

dnakit.databases.reactome_analysis_pathway_enrichment(*, identifiers, page_size=None, include_disease=None, projection=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`identifiers`	string	必填	Newline-separated list of gene/protein identifiers. Supports gene symbols (TP53, BRCA1), UniProt IDs (P04637, P38398), or Ensembl IDs. Example: 'TP53\nBRCA1\nCDH1\nEGFR\nKRAS'.
`page_size`	integer \| null	None	Number of pathways to return (default 20, max 50).
`include_disease`	boolean \| null	None	Include disease pathways in results (default true).
`projection`	boolean \| null	None	Project identifiers to human Reactome pathways for cross-species analysis (default true).
`verbose`	bool	True	运行提示开关。

dnakit.databases.string_functional_enrichment(*, protein_ids, species=None, category=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`protein_ids`	array	必填	List of protein identifiers (UniProt IDs, gene names, Ensembl IDs). Minimum 3 proteins recommended for meaningful enrichment. {"items": {"type": "string"}, "minItems": 2}
`species`	integer	None	NCBI taxonomy ID (default: 9606 for human)
`category`	string	None	Enrichment category: 'Process' (GO Biological Process), 'Component' (GO Cellular Component), 'Function' (GO Molecular Function), 'KEGG', 'Reactome', 'WikiPathways', 'COMPARTMENTS', 'TISSUES', 'DISEASES'
`verbose`	bool	True	运行提示开关。

dnakit.databases.string_get_functional_enrichment(*, identifiers, species=9606, category=None, verbose=True)

参数	类型	必填 / 默认值	说明与约束
`identifiers`	string	必填	以换行或回车分隔的蛋白标识；将转换成 STRING 标识列表。
`species`	integer	9606	物种名或 Taxonomy ID；类型与支持值取决于当前接口。
`category`	string	None	分类或结果类别，按当前接口的枚举/来源定义填写。
`verbose`	bool	True	运行提示开关。