analytical-grounding

Retrieve pathway members, cell-type markers, and genomic interval overlaps from biological databases.

475|61|Updated May 28, 2026

Search Tags:#genomics #pathway analysis #cell type markers #genomic intervals #biological information

Ready to run

npx skills add https://github.com/exon-research/genomi --skill analytical-grounding

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: analytical-grounding
Source: https://github.com/exon-research/genomi/tree/main/skills/analytical-grounding
Command: npx skills add https://github.com/exon-research/genomi --skill analytical-grounding

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires genomic databases, GENCODE, ENCODE, biological databases, and includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve?

Analytical Grounding simplifies accessing and interpreting complex genetic and biological data by retrieving essential information such as pathway members, cell type markers, and genomic feature overlaps.

Core Features & Use Cases

Retrieve Pathway Members: Extract member genes from defined pathways (Reactome, KEGG).
Access Cell-Type Markers: Get marker-gene records for specified cell types.
Feature Overlaps: Obtain genomic interval overlaps with declared annotation files.
Use Case: If you are analyzing a gene set and need to understand its membership in a specific pathway, Analytical Grounding can provide that information quickly.

Quick Start

To retrieve the member genes of a Reactome pathway, use: pathway.retrieve_members --pathway_id_or_name R-HSA-70635

Frequently Asked Questions about analytical-grounding

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I retrieve member genes from a Reactome or KEGG pathway?▼

To retrieve pathway members, you can extract member genes from defined Reactome or KEGG pathways using the pathway retrieval command with a specific pathway identifier or name.

What is the best way to get cell-type marker genes for genomic analysis?▼

The best way to get cell-type markers is by accessing marker-gene records from biological databases like HPA and CellMarker, which provide specific marker information for specified cell types.

How do I find genomic interval overlaps with annotation files?▼

You can find genomic interval overlaps by querying declared annotation files against genomic features, which requires access to relevant biological databases and tools like GENCODE or ENCODE.

Do I need GENCODE or ENCODE to perform genomic feature overlap analysis?▼

Yes, accessing relevant biological databases and tools like GENCODE or ENCODE is required to obtain genomic interval overlaps with declared annotation files for genomic feature overlap analysis.

Can I use this approach to understand gene set membership in biological pathways?▼

Yes, if you are analyzing a gene set and need to understand its membership in a specific pathway, this approach provides pathway membership information by extracting member genes from defined Reactome or KEGG pathways.

What databases are supported for retrieving biological and genetic information?▼

Supported databases include Reactome and KEGG for pathway members, HPA and CellMarker for cell-type markers, and GENCODE or ENCODE for genomic interval overlaps and feature annotations.