AN
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数据与复现
GS
gsea-enrichment-analysis
维护者 FreedomIntelligence · 最近更新 2026年4月1日
This skill covers gene set enrichment analysis (GSEA) and pathway enrichment workflows in OmicVerse. It provides critical guidance on the correct data formats and API usage patterns to avoid common errors.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/gsea-enrichment
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- This skill covers gene set enrichment analysis (GSEA) 、 pathway enrichment workflows in OmicVerse. It provides critical guidance on correct data formats 、 API usage patterns to avoid common errors。
- ov.utils.download_pathway_database()。
原始文档
SKILL.md 摘录
IMPORTANT: Use Dictionary Format, NOT File Path!
The ov.bulk.geneset_enrichment() function requires a dictionary of gene sets, NOT a file path string. You must first load the geneset file using ov.utils.geneset_prepare().
CORRECT usage:
## Step 2: Load geneset file into dictionary format - REQUIRED!
pathways_dict = ov.utils.geneset_prepare(
'genesets/GO_Biological_Process_2021.txt', # or .gmt file
organism='Human' # or 'Mouse'
)
## Step 3: Now run enrichment with the DICTIONARY
enr = ov.bulk.geneset_enrichment(
gene_list=deg_genes,
pathways_dict=pathways_dict, # Pass the DICTIONARY, not file path!
pvalue_type='auto',
organism='Human'
)
python
适用场景
- Use gsea-enrichment-analysis ，用于 single-cell 或 spatial omics analysis。
- Apply gsea-enrichment-analysis to 聚类，integration，或 trajectory workflows。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
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