vSPACE-AD LLM GENiE

A Dash web application for visualizing single-cell RNA sequencing data with UMAP scatter plots and bubble plots.

Overview

This application provides an interactive interface for exploring single-cell RNA sequencing data, specifically designed for the LLM-Driven AFA project. It features:

UMAP visualization of cell clusters
Bubble plot visualization of gene expression across cell types
Interactive controls for data exploration
Support for real 10X Genomics data

Project Structure

app.py: Main Dash application
load_10x_data.py: Script for processing 10X Genomics data
assets/: Contains CSS and sample data
- custom.css: Custom styling for the application
- sample_data/: Directory containing processed data
design_document.md: Detailed design documentation
todo.md: Development tasks and progress

Setup and Installation

Clone this repository

Install dependencies:

pip install dash dash-bootstrap-components pandas numpy scanpy plotly

Run the application:
```
python app.py
```

Data Integration

The application can load and visualize 10X Genomics single-cell RNA sequencing data. To process your own data:

Place your 10X Genomics files (matrix.mtx.gz, features.tsv.gz, barcodes.tsv.gz) in a directory
Update the path in load_10x_data.py
Run the script to generate the processed data:
```
python load_10x_data.py
```

Features

UMAP Scatter Plot: Visualize cells in 2D space with coloring by gene expression or cell type
Bubble Plot: Compare gene expression across different cell types
Interactive Controls: Filter cells, adjust visualization parameters, and select genes of interest
Statistics: View cell counts and distributions across cell types

chz17013/vspace-ad-llm-genie

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