cellink.tl.external.download_sclinker_references

cellink.tl.external.download_sclinker_references(out_dir='sclinker_references', tissue=None)

Download sc-linker reference files.

For 1000G files (PLINK, LD scores, weights, frq, HapMap3), use the cellink resource helpers instead — they download from Zenodo (https://zenodo.org/records/10515792) which is reliable and fast:

from cellink.resources import (
    get_1000genomes_ld_scores,
    get_1000genomes_ld_weights,
    get_1000genomes_plink_files,
    get_1000genomes_frq,
    get_1000genomes_hapmap3,
)

This function handles only the sc-linker-specific extras (enhancer-gene links, gene coordinates) which are only available via Google Cloud Storage:

gs://broad-alkesgroup-public/LDSCORE/Jagadeesh_Dey_sclinker/extras/

Parameters:

• out_dir (str | Path (default: 'sclinker_references')) – Root directory for downloaded files.

• tissue (str | None (default: None)) – Tissue code (e.g. "BLD"). None downloads all tissues.

• download_roadmap – Which enhancer-gene link files to download (default: all True).

• download_abc – Which enhancer-gene link files to download (default: all True).

• download_gene_coords – Which enhancer-gene link files to download (default: all True).

• download_bims – Kept for API compatibility but ignored — use the cellink resource helpers listed above instead.

• download_frq – Kept for API compatibility but ignored — use the cellink resource helpers listed above instead.

• download_weights – Kept for API compatibility but ignored — use the cellink resource helpers listed above instead.

• download_hapmap3 – Kept for API compatibility but ignored — use the cellink resource helpers listed above instead.

• download_baseline – Kept for API compatibility but ignored — use the cellink resource helpers listed above instead.

• chromosomes – Ignored (kept for API compatibility).

Return type:

dict[str, Path]