# harmstonlab/choy_et_al_deaf1 architecture

> Architecture diagram of the GitHub repository harmstonlab/choy_et_al_deaf1, generated by GitDiagram from its file tree, README and a sample of source files (last updated 2026-09-29). It is an AI-made overview: check details against the source.

- Interactive diagram: https://gitdiagram.com/harmstonlab/choy_et_al_deaf1
- Repository: https://github.com/harmstonlab/choy_et_al_deaf1

## Overview

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: [`Analysis/Annotate.qmd`](https://github.com/harmstonlab/choy_et_al_deaf1/blob/main/Analysis/Annotate.qmd) (Peak annotation), [`ChIPQC/ChIPQC.qmd`](https://github.com/harmstonlab/choy_et_al_deaf1/blob/main/ChIPQC/ChIPQC.qmd) (ChIP QC report), [`Analysis/GREAT.qmd`](https://github.com/harmstonlab/choy_et_al_deaf1/blob/main/Analysis/GREAT.qmd) (GREAT enrichment), [`peaks`](https://github.com/harmstonlab/choy_et_al_deaf1/tree/main/peaks) (Peak datasets)

## Diagram (Mermaid)

```mermaid
flowchart TD

subgraph group_inputs["Analysis inputs"]
  node_peaksets["Peak datasets"]
  node_metadata["ChIP metadata"]
end

subgraph group_analysis["Analysis notebooks"]
  node_annotate["Peak annotation<br/>[Annotate.qmd]"]
  node_great["GREAT enrichment<br/>[GREAT.qmd]"]
  node_promoter["Promoter plot<br/>[PromoterPlot.qmd]"]
  node_meme["MEME analysis<br/>[MEME.qmd]"]
end

subgraph group_results["Analysis results"]
  node_annotated["Annotation outputs"]
  node_greatout["GREAT results"]
end

subgraph group_qc["Quality control"]
  node_chipqc["ChIP QC report<br/>[ChIPQC.qmd]"]
  node_qcdata["QC report data"]
end

node_researcher(("Researcher"))

node_researcher -->|"runs annotation"| node_annotate
node_researcher -->|"runs enrichment"| node_great
node_researcher -->|"runs plotting"| node_promoter
node_researcher -->|"runs analysis"| node_meme
node_researcher -->|"runs QC"| node_chipqc
node_peaksets -->|"peak input"| node_annotate
node_annotate -->|"writes results"| node_annotated
node_great -->|"writes results"| node_greatout
node_metadata -->|"metadata input"| node_chipqc
node_chipqc -->|"produces report"| node_qcdata

click node_peaksets "https://github.com/harmstonlab/choy_et_al_deaf1/tree/main/peaks"
click node_metadata "https://github.com/harmstonlab/choy_et_al_deaf1/blob/main/meta/chipqc_metadata.csv"
click node_annotate "https://github.com/harmstonlab/choy_et_al_deaf1/blob/main/Analysis/Annotate.qmd"
click node_great "https://github.com/harmstonlab/choy_et_al_deaf1/blob/main/Analysis/GREAT.qmd"
click node_promoter "https://github.com/harmstonlab/choy_et_al_deaf1/blob/main/Analysis/PromoterPlot.qmd"
click node_meme "https://github.com/harmstonlab/choy_et_al_deaf1/blob/main/Analysis/MEME.qmd"
click node_annotated "https://github.com/harmstonlab/choy_et_al_deaf1/tree/main/Analysis/output"
click node_greatout "https://github.com/harmstonlab/choy_et_al_deaf1/tree/main/Analysis"
click node_chipqc "https://github.com/harmstonlab/choy_et_al_deaf1/blob/main/ChIPQC/ChIPQC.qmd"
click node_qcdata "https://github.com/harmstonlab/choy_et_al_deaf1/tree/main/ChIPQC/ChIPQCreport"

classDef toneNeutral fill:#f8fafc,stroke:#334155,stroke-width:1.5px,color:#0f172a
classDef toneBlue fill:#dbeafe,stroke:#2563eb,stroke-width:1.5px,color:#172554
classDef toneAmber fill:#fef3c7,stroke:#d97706,stroke-width:1.5px,color:#78350f
classDef toneMint fill:#dcfce7,stroke:#16a34a,stroke-width:1.5px,color:#14532d
classDef toneRose fill:#ffe4e6,stroke:#e11d48,stroke-width:1.5px,color:#881337
classDef toneIndigo fill:#e0e7ff,stroke:#4f46e5,stroke-width:1.5px,color:#312e81
classDef toneTeal fill:#ccfbf1,stroke:#0f766e,stroke-width:1.5px,color:#134e4a
class node_peaksets,node_metadata toneBlue
class node_annotate,node_great,node_promoter,node_meme toneAmber
class node_annotated,node_greatout toneMint
class node_chipqc,node_qcdata toneRose
class node_researcher toneIndigo
```

## Components

### Analysis inputs

- [Peak datasets](https://github.com/harmstonlab/choy_et_al_deaf1/tree/main/peaks): `peaks`
- [ChIP metadata](https://github.com/harmstonlab/choy_et_al_deaf1/blob/main/meta/chipqc_metadata.csv): `meta/chipqc_metadata.csv`

### Analysis notebooks

- [Peak annotation](https://github.com/harmstonlab/choy_et_al_deaf1/blob/main/Analysis/Annotate.qmd): `Analysis/Annotate.qmd`
- [GREAT enrichment](https://github.com/harmstonlab/choy_et_al_deaf1/blob/main/Analysis/GREAT.qmd): `Analysis/GREAT.qmd`
- [Promoter plot](https://github.com/harmstonlab/choy_et_al_deaf1/blob/main/Analysis/PromoterPlot.qmd): `Analysis/PromoterPlot.qmd`
- [MEME analysis](https://github.com/harmstonlab/choy_et_al_deaf1/blob/main/Analysis/MEME.qmd): `Analysis/MEME.qmd`

### Analysis results

- [Annotation outputs](https://github.com/harmstonlab/choy_et_al_deaf1/tree/main/Analysis/output): `Analysis/output`
- [GREAT results](https://github.com/harmstonlab/choy_et_al_deaf1/tree/main/Analysis): `Analysis`

### Quality control

- [ChIP QC report](https://github.com/harmstonlab/choy_et_al_deaf1/blob/main/ChIPQC/ChIPQC.qmd): `ChIPQC/ChIPQC.qmd`
- [QC report data](https://github.com/harmstonlab/choy_et_al_deaf1/tree/main/ChIPQC/ChIPQCreport): `ChIPQC/ChIPQCreport`

### Other components

- **Researcher**

## Connections

- 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