Rebuild base-GRNs for SC-beta cell types

[adamklie]

Context

Latest code: manuscripts/ChromBetaNet/bin/8_GRN. Needs further development.

Tasks

• Prune edges with SCENIC-like approach
• In silico TF perturbations
• In silico cRE perturbations (TBD)

[adamklie]

Dependencies

• Blocked by Retrain ChromBPNet models at different resolutions #1 (needs retrained ChromBPNet for TF-to-peak links)
• Feeds into Repeat and expand variant effect predictions #15 (variant effect predictions), Prioritize cREs for CRISPRi validation #16 (cRE prioritization)

[adamklie]

Notes from project reorganization (2026-03-23)

GRN building plans filed in gene-networks/README.md:

Planned analyses:

• Gene program clustering
• All-treatment DEGs and IFNg DEGs
• Gene set enrichment and disease enrichment
• WGCNA
• SCENIC+ on SC-islet dataset
• cRE-gene link basic analyses

Gene set analysis pipeline use cases documented in gene-networks/gsa_use_cases.md — covers the 6-step GSA pipeline (validate → enrichment → regulators → variants → regression → LLM aggregation) and input format specs.

[adamklie]

Status Update (2026-04-09)

Blocked on #1 (ChromBPNet). Deferred.