analytical-grounding

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.

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.

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.

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.

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.

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.