crescendo-scatac-cre-analysis
CommunityReveal CRE shifts inside ATAC peaks.
System Documentation
What problem does it solve?
CREscendo detects differential cis-regulatory element (CRE) usage within individual scATAC peaks by projecting ENCODE SCREEN cCREs onto peaks and testing Tn5 cleavage counts per sub-element via chi-square. Use when peak-level DA is weak or ambiguous and you suspect within-peak regulatory shifts (e.g., different enhancers driving same gene in cDC1A vs cDC1B). For peak-level differential accessibility use Signac/ArchR FindMarkers; for motif-level activity use chromvar-motif-accessibility.
Core Features & Use Cases
- Detect differential CRE usage within peaks by projecting external CRE catalogs onto peaks and counting Tn5 cleavage per CRE segment, enabling finer-grained regulatory interpretation.
- Works when peak-level differential accessibility is weak or ambiguous; reveals CRE switching inside peaks and ties changes to specific CREs with downstream analyses (motif-level activity, footprinting, peak-to-gene linking).
- Quick-start example: provide a real-world scenario where CRE switching explains gene expression changes despite similar peak DA.
Quick Start
Load your scATAC peaks, load ENCODE cCRE annotations, and run the PrepareCREscendoObject and CREtest workflow to identify changing CREs.
Dependency Matrix
Required Modules
None requiredComponents
Standard package💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: crescendo-scatac-cre-analysis Download link: https://github.com/tony-zhelonkin/SciAgent-toolkit/archive/main.zip#crescendo-scatac-cre-analysis Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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