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crescendo-scatac-cre-analysis

Project ENCODE cCRE catalogs onto scATAC peaks and count sub-peak segments.

1|Updated Nov 20, 2025
Search Tags:#cre#scatac-seq#crescendo#cis-regulatory-elements#encode-screen#sub-peak-analysis
One-click install
npx skills add https://github.com/tony-zhelonkin/SciAgent-toolkit --skill crescendo-scatac-cre-analysis
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: crescendo-scatac-cre-analysis
Source: https://github.com/tony-zhelonkin/SciAgent-toolkit/tree/main/skills/crescendo-scatac-cre-analysis
Command: npx skills add https://github.com/tony-zhelonkin/SciAgent-toolkit --skill crescendo-scatac-cre-analysis

SYSTEM DOCUMENTATION & REQUIREMENTS

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.

Frequently Asked Questions about crescendo-scatac-cre-analysis

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I detect differential cis-regulatory element usage within scATAC peaks when peak-level accessibility is weak?▼

CREscendo identifies differential CRE usage by projecting ENCODE cCRE annotations onto scATAC peaks and counting Tn5 cleavage counts per sub-peak CRE segment via chi-square tests, producing per-peak and per-CRE contribution statistics for weak or ambiguous peak-level accessibility.

When should I use sub-peak CRE analysis instead of standard peak-level differential accessibility?▼

Sub-peak CRE analysis is needed when peak-level differential accessibility is weak or ambiguous and you suspect within-peak regulatory shifts, like different enhancers driving the same gene across cell subtypes. It reveals CRE switching that standard peak-level differential accessibility tests miss.

How do I project ENCODE SCREEN cCREs onto scATAC peaks for differential testing?▼

Project ENCODE SCREEN cCREs onto scATAC peaks by loading both datasets and running the PrepareCREscendoObject and CREtest workflow. This counts Tn5 cleavage fragments per sub-peak CRE segment to generate per-peak and per-CRE contribution statistics via chi-square testing.

What is the difference between CREscendo and peak-level differential accessibility tools like FindMarkers?▼

CREscendo detects within-peak differential cis-regulatory element usage by testing sub-peak CRE segments via chi-square, whereas Signac or ArchR FindMarkers analyze peak-level differential accessibility. Use CREscendo when peak-level DA is weak or ambiguous but within-peak regulatory shifts are suspected.

Do I need ENCODE cCRE annotations and fragment files to run CREscendo?▼

Yes, CREscendo requires ENCODE cCRE annotations and fragment handling to project external CRE catalogs onto scATAC peaks. These inputs enable counting Tn5 cleavage events per sub-peak CRE segment for the chi-square differential testing workflow.

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