Macrophage ATAC-seq Visualization App

An interactive R Shiny application for visualizing and analyzing ATAC-seq data from macrophage samples. This application provides a user-friendly interface to explore chromatin accessibility patterns in macrophages.

Table of Contents

• Features
• Quick Start
• Installation
• Usage
• Data Description
• Docker Deployment
• Configuration
• Contributing

Features

• Interactive visualization of ATAC-seq peaks
• Analysis of differential accessibility between conditions
• Integration with gene expression data
• Dynamic filtering and sorting capabilities
• Customizable visualization parameters
• Export functionality for plots and data

Quick Start

Using Docker:

docker pull rohitrrj/macrophage-atac
docker run -p 3838:3838 rohitrrj/macrophage-atac

The app will be available at: http://localhost:3838

Installation

Local Installation

1. Clone the repository:

git clone https://github.com/rohitrrj/macrophage_atac.git
cd macrophage_atac

2. Install R dependencies:

install.packages(c("shiny", "ggplot2", "DT", "plotly"))

3. Run the app:

shiny::runApp("app")

Docker Installation

Build the Docker image:

docker build -t macrophage-atac .

Usage

1. Launch the application
2. Upload or select pre-loaded data
3. Use the sidebar controls to:
   • Select samples/conditions
   • Adjust visualization parameters
   • Filter data points
4. Interact with plots and tables
5. Export results as needed

Data Description

The application works with:

• Processed ATAC-seq peak files
• VST-normalized count matrix (vstNormalizedCounts_Macrophage.txt)
• Gene annotations (Gene_Symbols.txt)
• Differential accessibility results (HCvsCAD.txt)

Data Format Requirements

Peak Files:

chromosome start end signal
chr1    1000    1500    5.2
chr1    2000    2500    3.1
...

Count Matrix:

GeneID Sample1 Sample2 Sample3
GENE1  10.5    11.2    9.8
GENE2  8.7     7.9     8.1
...

Docker Deployment

The application is containerized using Docker for easy deployment:

FROM rocker/shiny:4.1.0

# Install system dependencies
RUN apt-get update && apt-get install -y \
    libcurl4-gnutls-dev \
    libssl-dev

# Copy application files
COPY app /srv/shiny-server/app
COPY shiny-server.sh /usr/bin/shiny-server.sh
COPY shiny-customized.config /etc/shiny-server/shiny-server.conf

# Set permissions
RUN chmod +x /usr/bin/shiny-server.sh

# Expose port
EXPOSE 3838

# Start Shiny server
CMD ["/usr/bin/shiny-server.sh"]

Configuration

Shiny Server Configuration

The application uses a custom Shiny server configuration (shiny-customized.config):

run_as shiny;
preserve_logs true;
access_log /var/log/shiny-server/access.log tiny;
server {
  listen 3838;
  location / {
    site_dir /srv/shiny-server/app;
    log_dir /var/log/shiny-server;
    directory_index on;
  }
}

Application Settings

Modify app/app.R for:

• Maximum upload size
• Cache settings
• Plot parameters
• Default filters

Contributing

1. Fork the repository
2. Create a feature branch
3. Make your changes
4. Submit a pull request

Development Guidelines

• Follow R code style guidelines
• Add tests for new features
• Update documentation
• Test Docker deployment

License

This project is licensed under the MIT License - see the LICENSE file for details.

Applications

This visualization tool has been used in the following publications:

1. "PD-1 combination therapy with IL-2 modifies CD8+ T cell exhaustion program"

   • Nature. 2022 Oct;610(7933):737-743
   • DOI: 10.1038/s41586-022-05257-0
   • PMID: 36215562
   • Used for visualizing chromatin accessibility changes in exhausted T cells

2. "Epigenetic signature of PD-1+ TCF1+ CD8 T cells that act as resource cells during chronic viral infection"

   • Proc Natl Acad Sci U S A. 2022 Feb 22;119(8):e2117314119
   • DOI: 10.1073/pnas.2117314119
   • PMID: 35085847
   • Used for interactive exploration of ATAC-seq peaks in T cell subsets

Code availability: ⭐ rohitrrj/macrophage_atac - Interactive visualization app for ATAC-seq data analysis

Acknowledgments

• Data processing pipeline: ATACseq_Pipeline
• R Shiny framework
• Supporting institutions and funding