# mrugakshi77/pss_scrna_biomarker_discovery architecture

> Architecture diagram of the GitHub repository mrugakshi77/pss_scrna_biomarker_discovery, generated by GitDiagram from its file tree, README and a sample of source files (last updated 2026-09-30). It is an AI-made overview: check details against the source.

- Interactive diagram: https://gitdiagram.com/mrugakshi77/pss_scrna_biomarker_discovery
- Repository: https://github.com/mrugakshi77/pss_scrna_biomarker_discovery

## Overview

This repository reproduces a pSS single-cell RNA-seq analysis and presents its results in a Shiny biomarker explorer. The documented workflow runs from GEO data download through quality control, normalization, dimensionality reduction, clustering, and differential expression; a preparation script extracts lightweight app data, which supports interactive visualization. The README documents these stages and app capabilities, but no source excerpts were available, so implementation-level calls and the exact use of individual data files cannot be verified.

Main entry points: [`pss_workflow.ipynb`](https://github.com/mrugakshi77/pss_scrna_biomarker_discovery/blob/main/pss_workflow.ipynb) (Single-cell analysis), [`prepare_app_data.r`](https://github.com/mrugakshi77/pss_scrna_biomarker_discovery/blob/main/prepare_app_data.r) (Data preparation), [`app_data.rds`](https://github.com/mrugakshi77/pss_scrna_biomarker_discovery/blob/main/app_data.rds) (Prepared app data), [`App.R`](https://github.com/mrugakshi77/pss_scrna_biomarker_discovery/blob/main/App.R) (Shiny dashboard)

## Diagram (Mermaid)

```mermaid
flowchart TD

subgraph group_analysis["Analysis pipeline"]
  node_pipeline["Single-cell analysis<br/>[pss_workflow.ipynb]"]
end

subgraph group_appdata["App data"]
  node_prepare["Data preparation<br/>[prepare_app_data.r]"]
  node_bundle[("Prepared app data<br/>[app_data.rds]")]
end

subgraph group_explorer["Interactive explorer"]
  node_dashboard["Shiny dashboard<br/>[App.R]"]
end

node_geo[("GEO dataset")]

node_geo -->|"downloads data"| node_pipeline
node_pipeline -.->|"provides analysis results"| node_prepare
node_prepare -->|"extracts data"| node_bundle
node_bundle -.->|"supplies app data"| node_dashboard

click node_pipeline "https://github.com/mrugakshi77/pss_scrna_biomarker_discovery/blob/main/pss_workflow.ipynb"
click node_prepare "https://github.com/mrugakshi77/pss_scrna_biomarker_discovery/blob/main/prepare_app_data.r"
click node_bundle "https://github.com/mrugakshi77/pss_scrna_biomarker_discovery/blob/main/app_data.rds"
click node_dashboard "https://github.com/mrugakshi77/pss_scrna_biomarker_discovery/blob/main/App.R"

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_pipeline toneBlue
class node_prepare,node_bundle,node_geo toneAmber
class node_dashboard toneMint
```

## Components

### Analysis pipeline

- [Single-cell analysis](https://github.com/mrugakshi77/pss_scrna_biomarker_discovery/blob/main/pss_workflow.ipynb): `pss_workflow.ipynb`

### App data

- [Data preparation](https://github.com/mrugakshi77/pss_scrna_biomarker_discovery/blob/main/prepare_app_data.r): `prepare_app_data.r`
- [Prepared app data](https://github.com/mrugakshi77/pss_scrna_biomarker_discovery/blob/main/app_data.rds): `app_data.rds`

### Interactive explorer

- [Shiny dashboard](https://github.com/mrugakshi77/pss_scrna_biomarker_discovery/blob/main/App.R): `App.R`

### Other components

- **GEO dataset**

## Connections

- GEO dataset → Single-cell analysis: downloads data (evidence: `README.md`)
- Single-cell analysis → Data preparation: provides analysis results
- Data preparation → Prepared app data: extracts data (evidence: `README.md`)
- Prepared app data → Shiny dashboard: supplies app data