cellink.tl.external.download_sclinker_enhancer_links

cellink.tl.external.download_sclinker_enhancer_links(out_dir='sclinker_refs', *, tissue=None, chromosomes=None)

Download the sc-linker enhancer-gene reference files from GCS.

Downloads the two large combined files that cellink then filters by tissue:

• RoadmapUABCannot_regions_to_genes.txt.gz: all-tissue Roadmap enhancer-gene activity scores.

• AllPredictions.AvgHiC.ABC0.015.minus150.withcolnames.ForABCPaper.txt.gz: all-tissue ABC model predictions.

• Roadmap_map_EID_names.txt: Roadmap EID -> tissue name mapping.

The per-tissue files (Roadmap_BLD_E.txt.gz etc.) do not exist in the bucket. They are produced on-the-fly by load_roadmap_links() and load_abc_links() when the downloaded combined files is passed.

Parameters:

• out_dir (str | Path (default: 'sclinker_refs')) – Directory to download files into.

• tissue (str | None (default: None)) – Accepted for API compatibility but ignored — the combined files cover all tissues. Pass tissue to load_roadmap_links() / load_abc_links() to filter after downloading.

• chromosomes (list[int] | None (default: None)) – Unused — kept for API consistency.

Return type:

dict[str, Path]

Returns:

dict with keys: "roadmap" → Path to RoadmapUABCannot_regions_to_genes.txt.gz "abc" → Path to AllPredictions.AvgHiC.ABC0.015...txt.gz "roadmap_eid" → Path to Roadmap_map_EID_names.txt