How harmstonlab/choy_et_al_deaf1 works
This repository contains reproducibility materials for Choy et al. 2025, not a software service. The documented workflow is to use the analysis notebooks to annotate Deaf1 ChIP-seq peaks, perform GREAT enrichment analysis, and plot Mtor promoter enrichment; separate ChIPQC materials report quality control. The tree also includes peak inputs, metadata, and generated annotation/enrichment outputs. Notebook contents were not sampled, so links from analyses to particular inputs, external tools, or outputs are not asserted beyond the documented capabilities.
Main entry points: Annotate.qmd Peak annotation · ChIPQC.qmd ChIP QC report · GREAT.qmd GREAT enrichment · peaks Peak datasets
Components 11
Analysis inputs
- Peak datasets
peaks - ChIP metadata
meta/chipqc_metadata.csv
Analysis notebooks
- Peak annotation
Analysis/Annotate.qmd - GREAT enrichment
Analysis/GREAT.qmd - Promoter plot
Analysis/PromoterPlot.qmd - MEME analysis
Analysis/MEME.qmd
Analysis results
- Annotation outputs
Analysis/output - GREAT results
Analysis
Quality control
- ChIP QC report
ChIPQC/ChIPQC.qmd - QC report data
ChIPQC/ChIPQCreport
Other components
- Researcher
Connections 10
- Researcher → Peak annotation: runs annotation
- Researcher → GREAT enrichment: runs enrichment
- Researcher → Promoter plot: runs plotting
- Researcher → MEME analysis: runs analysis
- Researcher → ChIP QC report: runs QC
- Peak datasets → Peak annotation: peak input
- Peak annotation → Annotation outputs: writes results
- GREAT enrichment → GREAT results: writes results
- ChIP metadata → ChIP QC report: metadata input
- ChIP QC report → QC report data: produces report