NAP: Network Analysis Profiler

A mediator for shaking hands between graph theory and systems biology.

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📖 Table of Contents

1. Overview
2. Key Features
3. Installation
4. Usage
5. Publications
6. License

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📝 Overview

NAP is a Shiny-based web application designed to profile the topology of medium-scale networks (up to a few thousand edges) and facilitate direct comparison through an intuitive interface. It bridges graph-theoretical metrics with systems biology needs, enabling users to explore, rank, and compare network topology seamlessly.

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🚀 Key Features

• Topological Exploration: Compute and visualize metrics such as degree, betweenness, closeness, clustering coefficient and more.
• Node & Edge Ranking: Rank elements by any computed metric and export results as tables or plots.
• Multi-Network Comparison: Load multiple networks simultaneously to compare topological properties side-by-side.
• Feature Distributions: Plot distributions of any topological feature across networks.
• Feature Correlation: Generate scatter plots of one metric against another to uncover relationships.
• Dynamic & Static Layouts: Visualize networks using layouts like Fruchterman–Reingold, Kamada–Kawai, circular, grid, and interactive 3D layers.

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🛠 Installation

Clone & Run Locally

git clone https://github.com/PavlopoulosLab/NAP.git
cd NAP

# In R console or RStudio:
source("install_dependencies.R")   # install required R packages
shiny::runApp(port = 3838)         # launch the app

Online Demo

Access NAP directly at: https://pavlopoulos-lab-services.org/shiny/app/nap

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💻 Usage

1. Upload one or more network edge-list files (tab-delimited).
2. Select topological metrics to compute and visualize.
3. Compare metric distributions and rankings across uploaded networks.
4. Explore interactive network views, adjust layouts, and export publication-ready figures.

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📚 Publications

• The Network Analysis Profiler (NAP v2.0): A web tool for visual topological comparison between multiple networks Koutrouli M., Theodosiou T., Iliopoulos I., Pavlopoulos G.A. EMBnet.journal, 2021 May;26:e943. doi: 10.14806/ej.26.0.943

• NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks Theodosiou T., Efstathiou G., Papanikolaou N., Kyrpides N.C., Bagos P.G., Iliopoulos I., Pavlopoulos G.A. BMC Research Notes, 2017;10:278. doi: 10.1186/s13104-017-2607-8 PMID: 28705239

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📄 License

This project is released under the MIT License. See the LICENSE file for details.