BranchesTags

Repository files navigation

R-CMD-checkShiny AppLicense: MIT

NORMA: The Network Makeup Artist

A web tool for interactive network annotation visualization and topological analysis.

📖 Table of Contents

  1. Overview
  2. Key Features
  3. Installation
  4. Usage
  5. Input Formats
  6. Examples & Demo Data
  7. Contact & Support
  8. Publications
  9. License

📝 Overview

NORMA (Network Makeup Artist) is a Shiny-based web application that lets you:

  • Visualize multiple networks and their annotations (e.g., GO terms, pathway enrichments)
  • Overlay annotations as pie-chart nodes or convex-hull “venn” shapes
  • Detect communities automatically when no annotations are provided
  • Refine layouts for optimal group separation with common graph algorithms
  • Highlight and export publication-quality figures interactively
  • Compare network topology metrics across different datasets

🚀 Key Features

  • Multi-network support: Load and visualize several networks side by side.

  • Annotation overlays:

    • Pie-chart nodes for multi-category annotations
    • Convex-hulls for set-overlap style visualization

  • Community detection: Fast algorithms (e.g., Louvain, Infomap) for de novo grouping.

  • Flexible layouts: Fruchterman–Reingold, Kamada–Kawai, circular, grid, and more.

  • Interactive figure export: Customize colors, sizes, labels; download as PNG or PDF.

  • Topological analysis: Compute degree, clustering coefficient, betweenness, etc., and compare across networks.

🛠 Installation

  1. Install R (≥4.0)

  2. Install RStudio (optional, but recommended)

  3. Clone this repo

    git clone https://github.com/yourusername/NORMA.git
cd NORMA

  4. Install required packages

    # From your R console:
install.packages(c(
"shiny", "igraph", "visNetwork", "plotly",
"data.table", "DT", "RColorBrewer"
))

  5. Run the app

    # In RStudio or R console:shiny::runApp("path/to/NORMA")

💻 Usage

  • Online demo: Launch NORMA in your browser

  • Local: Once the app is running, use the sidebar to upload:

    • Network file (edge list or adjacency)
    • Annotation file (tab-delimited with node → category)

  • Toggle between “Pie-chart nodes” and “Convex-hulls” in Visualization.

  • Explore Layout, Annotation, and Analysis tabs for customization.

📂 Input Formats

  • Network:

    • Edge list: source<TAB>target
    • Adjacency matrix: CSV or TSV

  • Annotations:

    • Plain table:

      node_id<TAB>category1,category2,...

  • See the Help → Input File tab in the app for detailed examples.

📊 Examples & Demo Data

Download sample networks and annotation sets from the app’s Help → Examples tab or directly from our website. These include:

  • Human protein–protein interaction subnetworks
  • GO term enrichment outputs for test datasets
  • Synthetic networks demonstrating overlapping modules

📬 Contact & Support

For questions, issues, or feature requests, please email:

George A. Pavlopoulospavlopoulos@fleming.gr

Or open an issue on GitHub: https://github.com/yourusername/NORMA/issues

📚 Publications

  • NORMA: The Network Makeup Artist Koutrouli M., Karatzas E., Papanikolopoulou K., Pavlopoulos G.A. Genomics, Proteomics & Bioinformatics. 2022 Jun;20(3):578⎼586. Epub 2021 Jun 24. doi: 10.1016/j.gpb.2021.02.005 PMID: 34171457

  • The network makeup artist (NORMA-2.0): Distinguishing annotated groups in a network using innovative layout strategies Karatzas E., Koutrouli M., Baltoumas F.A., Papanikolopoulou K., Bouyioukos C., Pavlopoulos G.A. Bioinformatics Advances. 2022 May 13;2(1):vbac036. doi: 10.1093/bioadv/vbac036 PMID: 36699373

📄 License

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

About

Network annotation visualization

pavlopoulos-lab-services.org/shiny/app/norma

Resources

Readme
MIT license
Activity

Stars

18 stars

Watchers

2 watching

Forks

6 forks
Report repository

Releases

Packages

Contributors

Languages

, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
BranchesTags
Repository files navigation
R-CMD-checkShiny AppLicense: MIT
NORMA: The Network Makeup Artist
A web tool for interactive network annotation visualization and topological analysis.
📖 Table of Contents
  1. Overview
  2. Key Features
  3. Installation
  4. Usage
  5. Input Formats
  6. Examples & Demo Data
  7. Contact & Support
  8. Publications
  9. License
📝 Overview
NORMA (Network Makeup Artist) is a Shiny-based web application that lets you:
  • Visualize multiple networks and their annotations (e.g., GO terms, pathway enrichments)
  • Overlay annotations as pie-chart nodes or convex-hull “venn” shapes
  • Detect communities automatically when no annotations are provided
  • Refine layouts for optimal group separation with common graph algorithms
  • Highlight and export publication-quality figures interactively
  • Compare network topology metrics across different datasets
🚀 Key Features
  • Multi-network support: Load and visualize several networks side by side.
  • Annotation overlays:
    • Pie-chart nodes for multi-category annotations
    • Convex-hulls for set-overlap style visualization
  • Community detection: Fast algorithms (e.g., Louvain, Infomap) for de novo grouping.
  • Flexible layouts: Fruchterman–Reingold, Kamada–Kawai, circular, grid, and more.
  • Interactive figure export: Customize colors, sizes, labels; download as PNG or PDF.
  • Topological analysis: Compute degree, clustering coefficient, betweenness, etc., and compare across networks.
🛠 Installation
  1. Install R (≥4.0)
  2. Install RStudio (optional, but recommended)
  3. Clone this repo
    git clone https://github.com/yourusername/NORMA.git
cd NORMA
  4. Install required packages
    # From your R console:
install.packages(c(
"shiny", "igraph", "visNetwork", "plotly",
"data.table", "DT", "RColorBrewer"
))
  5. Run the app
    # In RStudio or R console:shiny::runApp("path/to/NORMA")
💻 Usage
  • Online demo: Launch NORMA in your browser
  • Local: Once the app is running, use the sidebar to upload:
    • Network file (edge list or adjacency)
    • Annotation file (tab-delimited with node → category)
  • Toggle between “Pie-chart nodes” and “Convex-hulls” in Visualization.
  • Explore Layout, Annotation, and Analysis tabs for customization.
📂 Input Formats
  • Network:
    • Edge list: source<TAB>target
    • Adjacency matrix: CSV or TSV
  • Annotations:
    • Plain table:
      node_id<TAB>category1,category2,...

  • See the Help → Input File tab in the app for detailed examples.
📊 Examples & Demo Data
Download sample networks and annotation sets from the app’s Help → Examples tab or directly from our website. These include:
  • Human protein–protein interaction subnetworks
  • GO term enrichment outputs for test datasets
  • Synthetic networks demonstrating overlapping modules
📬 Contact & Support
For questions, issues, or feature requests, please email:
George A. Pavlopoulospavlopoulos@fleming.gr
Or open an issue on GitHub:
https://github.com/yourusername/NORMA/issues
📚 Publications
  • NORMA: The Network Makeup Artist
Koutrouli M., Karatzas E., Papanikolopoulou K., Pavlopoulos G.A.
Genomics, Proteomics & Bioinformatics. 2022 Jun;20(3):578⎼586. Epub 2021 Jun 24.
doi: 10.1016/j.gpb.2021.02.005
PMID: 34171457
  • The network makeup artist (NORMA-2.0): Distinguishing annotated groups in a network using innovative layout strategies
Karatzas E., Koutrouli M., Baltoumas F.A., Papanikolopoulou K., Bouyioukos C., Pavlopoulos G.A.
Bioinformatics Advances. 2022 May 13;2(1):vbac036.
doi: 10.1093/bioadv/vbac036
PMID: 36699373
📄 License
This project is licensed under the MIT License – see the LICENSE file for details.
About
Network annotation visualization
pavlopoulos-lab-services.org/shiny/app/norma
Resources
Readme
MIT license
Activity
Stars
18 stars
Watchers
2 watching
Forks
6 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
R-CMD-checkShiny AppLicense: MIT
NORMA: The Network Makeup Artist
A web tool for interactive network annotation visualization and topological analysis.
📖 Table of Contents
  1. Overview
  2. Key Features
  3. Installation
  4. Usage
  5. Input Formats
  6. Examples & Demo Data
  7. Contact & Support
  8. Publications
  9. License
📝 Overview
NORMA (Network Makeup Artist) is a Shiny-based web application that lets you:
  • Visualize multiple networks and their annotations (e.g., GO terms, pathway enrichments)
  • Overlay annotations as pie-chart nodes or convex-hull “venn” shapes
  • Detect communities automatically when no annotations are provided
  • Refine layouts for optimal group separation with common graph algorithms
  • Highlight and export publication-quality figures interactively
  • Compare network topology metrics across different datasets
🚀 Key Features
  • Multi-network support: Load and visualize several networks side by side.
  • Annotation overlays:
    • Pie-chart nodes for multi-category annotations
    • Convex-hulls for set-overlap style visualization
  • Community detection: Fast algorithms (e.g., Louvain, Infomap) for de novo grouping.
  • Flexible layouts: Fruchterman–Reingold, Kamada–Kawai, circular, grid, and more.
  • Interactive figure export: Customize colors, sizes, labels; download as PNG or PDF.
  • Topological analysis: Compute degree, clustering coefficient, betweenness, etc., and compare across networks.
🛠 Installation
  1. Install R (≥4.0)
  2. Install RStudio (optional, but recommended)
  3. Clone this repo
    git clone https://github.com/yourusername/NORMA.git
cd NORMA
  4. Install required packages
    # From your R console:
install.packages(c(
"shiny", "igraph", "visNetwork", "plotly",
"data.table", "DT", "RColorBrewer"
))
  5. Run the app
    # In RStudio or R console:shiny::runApp("path/to/NORMA")
💻 Usage
  • Online demo: Launch NORMA in your browser
  • Local: Once the app is running, use the sidebar to upload:
    • Network file (edge list or adjacency)
    • Annotation file (tab-delimited with node → category)
  • Toggle between “Pie-chart nodes” and “Convex-hulls” in Visualization.
  • Explore Layout, Annotation, and Analysis tabs for customization.
📂 Input Formats
  • Network:
    • Edge list: source<TAB>target
    • Adjacency matrix: CSV or TSV
  • Annotations:
    • Plain table:
      node_id<TAB>category1,category2,...

  • See the Help → Input File tab in the app for detailed examples.
📊 Examples & Demo Data
Download sample networks and annotation sets from the app’s Help → Examples tab or directly from our website. These include:
  • Human protein–protein interaction subnetworks
  • GO term enrichment outputs for test datasets
  • Synthetic networks demonstrating overlapping modules
📬 Contact & Support
For questions, issues, or feature requests, please email:
George A. Pavlopoulospavlopoulos@fleming.gr
Or open an issue on GitHub:
https://github.com/yourusername/NORMA/issues
📚 Publications
  • NORMA: The Network Makeup Artist
Koutrouli M., Karatzas E., Papanikolopoulou K., Pavlopoulos G.A.
Genomics, Proteomics & Bioinformatics. 2022 Jun;20(3):578⎼586. Epub 2021 Jun 24.
doi: 10.1016/j.gpb.2021.02.005
PMID: 34171457
  • The network makeup artist (NORMA-2.0): Distinguishing annotated groups in a network using innovative layout strategies
Karatzas E., Koutrouli M., Baltoumas F.A., Papanikolopoulou K., Bouyioukos C., Pavlopoulos G.A.
Bioinformatics Advances. 2022 May 13;2(1):vbac036.
doi: 10.1093/bioadv/vbac036
PMID: 36699373
📄 License
This project is licensed under the MIT License – see the LICENSE file for details.
About
Network annotation visualization
pavlopoulos-lab-services.org/shiny/app/norma
Resources
Readme
MIT license
Activity
Stars
18 stars
Watchers
2 watching
Forks
6 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
R-CMD-checkShiny AppLicense: MIT
NORMA: The Network Makeup Artist
A web tool for interactive network annotation visualization and topological analysis.
📖 Table of Contents
  1. Overview
  2. Key Features
  3. Installation
  4. Usage
  5. Input Formats
  6. Examples & Demo Data
  7. Contact & Support
  8. Publications
  9. License
📝 Overview
NORMA (Network Makeup Artist) is a Shiny-based web application that lets you:
  • Visualize multiple networks and their annotations (e.g., GO terms, pathway enrichments)
  • Overlay annotations as pie-chart nodes or convex-hull “venn” shapes
  • Detect communities automatically when no annotations are provided
  • Refine layouts for optimal group separation with common graph algorithms
  • Highlight and export publication-quality figures interactively
  • Compare network topology metrics across different datasets
🚀 Key Features
  • Multi-network support: Load and visualize several networks side by side.
  • Annotation overlays:
    • Pie-chart nodes for multi-category annotations
    • Convex-hulls for set-overlap style visualization
  • Community detection: Fast algorithms (e.g., Louvain, Infomap) for de novo grouping.
  • Flexible layouts: Fruchterman–Reingold, Kamada–Kawai, circular, grid, and more.
  • Interactive figure export: Customize colors, sizes, labels; download as PNG or PDF.
  • Topological analysis: Compute degree, clustering coefficient, betweenness, etc., and compare across networks.
🛠 Installation
  1. Install R (≥4.0)
  2. Install RStudio (optional, but recommended)
  3. Clone this repo
    git clone https://github.com/yourusername/NORMA.git
cd NORMA
  4. Install required packages
    # From your R console:
install.packages(c(
"shiny", "igraph", "visNetwork", "plotly",
"data.table", "DT", "RColorBrewer"
))
  5. Run the app
    # In RStudio or R console:shiny::runApp("path/to/NORMA")
💻 Usage
  • Online demo: Launch NORMA in your browser
  • Local: Once the app is running, use the sidebar to upload:
    • Network file (edge list or adjacency)
    • Annotation file (tab-delimited with node → category)
  • Toggle between “Pie-chart nodes” and “Convex-hulls” in Visualization.
  • Explore Layout, Annotation, and Analysis tabs for customization.
📂 Input Formats
  • Network:
    • Edge list: source<TAB>target
    • Adjacency matrix: CSV or TSV
  • Annotations:
    • Plain table:
      node_id<TAB>category1,category2,...

  • See the Help → Input File tab in the app for detailed examples.
📊 Examples & Demo Data
Download sample networks and annotation sets from the app’s Help → Examples tab or directly from our website. These include:
  • Human protein–protein interaction subnetworks
  • GO term enrichment outputs for test datasets
  • Synthetic networks demonstrating overlapping modules
📬 Contact & Support
For questions, issues, or feature requests, please email:
George A. Pavlopoulospavlopoulos@fleming.gr
Or open an issue on GitHub:
https://github.com/yourusername/NORMA/issues
📚 Publications
  • NORMA: The Network Makeup Artist
Koutrouli M., Karatzas E., Papanikolopoulou K., Pavlopoulos G.A.
Genomics, Proteomics & Bioinformatics. 2022 Jun;20(3):578⎼586. Epub 2021 Jun 24.
doi: 10.1016/j.gpb.2021.02.005
PMID: 34171457
  • The network makeup artist (NORMA-2.0): Distinguishing annotated groups in a network using innovative layout strategies
Karatzas E., Koutrouli M., Baltoumas F.A., Papanikolopoulou K., Bouyioukos C., Pavlopoulos G.A.
Bioinformatics Advances. 2022 May 13;2(1):vbac036.
doi: 10.1093/bioadv/vbac036
PMID: 36699373
📄 License
This project is licensed under the MIT License – see the LICENSE file for details.
About
Network annotation visualization
pavlopoulos-lab-services.org/shiny/app/norma
Resources
Readme
MIT license
Activity
Stars
18 stars
Watchers
2 watching
Forks
6 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
BranchesTags
Repository files navigation
R-CMD-checkShiny AppLicense: MIT
NORMA: The Network Makeup Artist
A web tool for interactive network annotation visualization and topological analysis.
📖 Table of Contents
  1. Overview
  2. Key Features
  3. Installation
  4. Usage
  5. Input Formats
  6. Examples & Demo Data
  7. Contact & Support
  8. Publications
  9. License
📝 Overview
NORMA (Network Makeup Artist) is a Shiny-based web application that lets you:
  • Visualize multiple networks and their annotations (e.g., GO terms, pathway enrichments)
  • Overlay annotations as pie-chart nodes or convex-hull “venn” shapes
  • Detect communities automatically when no annotations are provided
  • Refine layouts for optimal group separation with common graph algorithms
  • Highlight and export publication-quality figures interactively
  • Compare network topology metrics across different datasets
🚀 Key Features
  • Multi-network support: Load and visualize several networks side by side.
  • Annotation overlays:
    • Pie-chart nodes for multi-category annotations
    • Convex-hulls for set-overlap style visualization
  • Community detection: Fast algorithms (e.g., Louvain, Infomap) for de novo grouping.
  • Flexible layouts: Fruchterman–Reingold, Kamada–Kawai, circular, grid, and more.
  • Interactive figure export: Customize colors, sizes, labels; download as PNG or PDF.
  • Topological analysis: Compute degree, clustering coefficient, betweenness, etc., and compare across networks.
🛠 Installation
  1. Install R (≥4.0)
  2. Install RStudio (optional, but recommended)
  3. Clone this repo
    git clone https://github.com/yourusername/NORMA.git
cd NORMA
  4. Install required packages
    # From your R console:
install.packages(c(
"shiny", "igraph", "visNetwork", "plotly",
"data.table", "DT", "RColorBrewer"
))
  5. Run the app
    # In RStudio or R console:shiny::runApp("path/to/NORMA")
💻 Usage
  • Online demo: Launch NORMA in your browser
  • Local: Once the app is running, use the sidebar to upload:
    • Network file (edge list or adjacency)
    • Annotation file (tab-delimited with node → category)
  • Toggle between “Pie-chart nodes” and “Convex-hulls” in Visualization.
  • Explore Layout, Annotation, and Analysis tabs for customization.
📂 Input Formats
  • Network:
    • Edge list: source<TAB>target
    • Adjacency matrix: CSV or TSV
  • Annotations:
    • Plain table:
      node_id<TAB>category1,category2,...

  • See the Help → Input File tab in the app for detailed examples.
📊 Examples & Demo Data
Download sample networks and annotation sets from the app’s Help → Examples tab or directly from our website. These include:
  • Human protein–protein interaction subnetworks
  • GO term enrichment outputs for test datasets
  • Synthetic networks demonstrating overlapping modules
📬 Contact & Support
For questions, issues, or feature requests, please email:
George A. Pavlopoulospavlopoulos@fleming.gr
Or open an issue on GitHub:
https://github.com/yourusername/NORMA/issues
📚 Publications
  • NORMA: The Network Makeup Artist
Koutrouli M., Karatzas E., Papanikolopoulou K., Pavlopoulos G.A.
Genomics, Proteomics & Bioinformatics. 2022 Jun;20(3):578⎼586. Epub 2021 Jun 24.
doi: 10.1016/j.gpb.2021.02.005
PMID: 34171457
  • The network makeup artist (NORMA-2.0): Distinguishing annotated groups in a network using innovative layout strategies
Karatzas E., Koutrouli M., Baltoumas F.A., Papanikolopoulou K., Bouyioukos C., Pavlopoulos G.A.
Bioinformatics Advances. 2022 May 13;2(1):vbac036.
doi: 10.1093/bioadv/vbac036
PMID: 36699373
📄 License
This project is licensed under the MIT License – see the LICENSE file for details.
About
Network annotation visualization
pavlopoulos-lab-services.org/shiny/app/norma
Resources
Readme
MIT license
Activity
Stars
18 stars
Watchers
2 watching
Forks
6 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
R-CMD-checkShiny AppLicense: MIT
NORMA: The Network Makeup Artist
A web tool for interactive network annotation visualization and topological analysis.
📖 Table of Contents
  1. Overview
  2. Key Features
  3. Installation
  4. Usage
  5. Input Formats
  6. Examples & Demo Data
  7. Contact & Support
  8. Publications
  9. License
📝 Overview
NORMA (Network Makeup Artist) is a Shiny-based web application that lets you:
  • Visualize multiple networks and their annotations (e.g., GO terms, pathway enrichments)
  • Overlay annotations as pie-chart nodes or convex-hull “venn” shapes
  • Detect communities automatically when no annotations are provided
  • Refine layouts for optimal group separation with common graph algorithms
  • Highlight and export publication-quality figures interactively
  • Compare network topology metrics across different datasets
🚀 Key Features
  • Multi-network support: Load and visualize several networks side by side.
  • Annotation overlays:
    • Pie-chart nodes for multi-category annotations
    • Convex-hulls for set-overlap style visualization
  • Community detection: Fast algorithms (e.g., Louvain, Infomap) for de novo grouping.
  • Flexible layouts: Fruchterman–Reingold, Kamada–Kawai, circular, grid, and more.
  • Interactive figure export: Customize colors, sizes, labels; download as PNG or PDF.
  • Topological analysis: Compute degree, clustering coefficient, betweenness, etc., and compare across networks.
🛠 Installation
  1. Install R (≥4.0)
  2. Install RStudio (optional, but recommended)
  3. Clone this repo
    git clone https://github.com/yourusername/NORMA.git
cd NORMA
  4. Install required packages
    # From your R console:
install.packages(c(
"shiny", "igraph", "visNetwork", "plotly",
"data.table", "DT", "RColorBrewer"
))
  5. Run the app
    # In RStudio or R console:shiny::runApp("path/to/NORMA")
💻 Usage
  • Online demo: Launch NORMA in your browser
  • Local: Once the app is running, use the sidebar to upload:
    • Network file (edge list or adjacency)
    • Annotation file (tab-delimited with node → category)
  • Toggle between “Pie-chart nodes” and “Convex-hulls” in Visualization.
  • Explore Layout, Annotation, and Analysis tabs for customization.
📂 Input Formats
  • Network:
    • Edge list: source<TAB>target
    • Adjacency matrix: CSV or TSV
  • Annotations:
    • Plain table:
      node_id<TAB>category1,category2,...

  • See the Help → Input File tab in the app for detailed examples.
📊 Examples & Demo Data
Download sample networks and annotation sets from the app’s Help → Examples tab or directly from our website. These include:
  • Human protein–protein interaction subnetworks
  • GO term enrichment outputs for test datasets
  • Synthetic networks demonstrating overlapping modules
📬 Contact & Support
For questions, issues, or feature requests, please email:
George A. Pavlopoulospavlopoulos@fleming.gr
Or open an issue on GitHub:
https://github.com/yourusername/NORMA/issues
📚 Publications
  • NORMA: The Network Makeup Artist
Koutrouli M., Karatzas E., Papanikolopoulou K., Pavlopoulos G.A.
Genomics, Proteomics & Bioinformatics. 2022 Jun;20(3):578⎼586. Epub 2021 Jun 24.
doi: 10.1016/j.gpb.2021.02.005
PMID: 34171457
  • The network makeup artist (NORMA-2.0): Distinguishing annotated groups in a network using innovative layout strategies
Karatzas E., Koutrouli M., Baltoumas F.A., Papanikolopoulou K., Bouyioukos C., Pavlopoulos G.A.
Bioinformatics Advances. 2022 May 13;2(1):vbac036.
doi: 10.1093/bioadv/vbac036
PMID: 36699373
📄 License
This project is licensed under the MIT License – see the LICENSE file for details.
About
Network annotation visualization
pavlopoulos-lab-services.org/shiny/app/norma
Resources
Readme
MIT license
Activity
Stars
18 stars
Watchers
2 watching
Forks
6 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
R-CMD-checkShiny AppLicense: MIT
NORMA: The Network Makeup Artist
A web tool for interactive network annotation visualization and topological analysis.
📖 Table of Contents
  1. Overview
  2. Key Features
  3. Installation
  4. Usage
  5. Input Formats
  6. Examples & Demo Data
  7. Contact & Support
  8. Publications
  9. License
📝 Overview
NORMA (Network Makeup Artist) is a Shiny-based web application that lets you:
  • Visualize multiple networks and their annotations (e.g., GO terms, pathway enrichments)
  • Overlay annotations as pie-chart nodes or convex-hull “venn” shapes
  • Detect communities automatically when no annotations are provided
  • Refine layouts for optimal group separation with common graph algorithms
  • Highlight and export publication-quality figures interactively
  • Compare network topology metrics across different datasets
🚀 Key Features
  • Multi-network support: Load and visualize several networks side by side.
  • Annotation overlays:
    • Pie-chart nodes for multi-category annotations
    • Convex-hulls for set-overlap style visualization
  • Community detection: Fast algorithms (e.g., Louvain, Infomap) for de novo grouping.
  • Flexible layouts: Fruchterman–Reingold, Kamada–Kawai, circular, grid, and more.
  • Interactive figure export: Customize colors, sizes, labels; download as PNG or PDF.
  • Topological analysis: Compute degree, clustering coefficient, betweenness, etc., and compare across networks.
🛠 Installation
  1. Install R (≥4.0)
  2. Install RStudio (optional, but recommended)
  3. Clone this repo
    git clone https://github.com/yourusername/NORMA.git
cd NORMA
  4. Install required packages
    # From your R console:
install.packages(c(
"shiny", "igraph", "visNetwork", "plotly",
"data.table", "DT", "RColorBrewer"
))
  5. Run the app
    # In RStudio or R console:shiny::runApp("path/to/NORMA")
💻 Usage
  • Online demo: Launch NORMA in your browser
  • Local: Once the app is running, use the sidebar to upload:
    • Network file (edge list or adjacency)
    • Annotation file (tab-delimited with node → category)
  • Toggle between “Pie-chart nodes” and “Convex-hulls” in Visualization.
  • Explore Layout, Annotation, and Analysis tabs for customization.
📂 Input Formats
  • Network:
    • Edge list: source<TAB>target
    • Adjacency matrix: CSV or TSV
  • Annotations:
    • Plain table:
      node_id<TAB>category1,category2,...

  • See the Help → Input File tab in the app for detailed examples.
📊 Examples & Demo Data
Download sample networks and annotation sets from the app’s Help → Examples tab or directly from our website. These include:
  • Human protein–protein interaction subnetworks
  • GO term enrichment outputs for test datasets
  • Synthetic networks demonstrating overlapping modules
📬 Contact & Support
For questions, issues, or feature requests, please email:
George A. Pavlopoulospavlopoulos@fleming.gr
Or open an issue on GitHub:
https://github.com/yourusername/NORMA/issues
📚 Publications
  • NORMA: The Network Makeup Artist
Koutrouli M., Karatzas E., Papanikolopoulou K., Pavlopoulos G.A.
Genomics, Proteomics & Bioinformatics. 2022 Jun;20(3):578⎼586. Epub 2021 Jun 24.
doi: 10.1016/j.gpb.2021.02.005
PMID: 34171457
  • The network makeup artist (NORMA-2.0): Distinguishing annotated groups in a network using innovative layout strategies
Karatzas E., Koutrouli M., Baltoumas F.A., Papanikolopoulou K., Bouyioukos C., Pavlopoulos G.A.
Bioinformatics Advances. 2022 May 13;2(1):vbac036.
doi: 10.1093/bioadv/vbac036
PMID: 36699373
📄 License
This project is licensed under the MIT License – see the LICENSE file for details.
About
Network annotation visualization
pavlopoulos-lab-services.org/shiny/app/norma
Resources
Readme
MIT license
Activity
Stars
18 stars
Watchers
2 watching
Forks
6 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
BranchesTags
Repository files navigation
R-CMD-checkShiny AppLicense: MIT
NORMA: The Network Makeup Artist
A web tool for interactive network annotation visualization and topological analysis.
📖 Table of Contents
  1. Overview
  2. Key Features
  3. Installation
  4. Usage
  5. Input Formats
  6. Examples & Demo Data
  7. Contact & Support
  8. Publications
  9. License
📝 Overview
NORMA (Network Makeup Artist) is a Shiny-based web application that lets you:
  • Visualize multiple networks and their annotations (e.g., GO terms, pathway enrichments)
  • Overlay annotations as pie-chart nodes or convex-hull “venn” shapes
  • Detect communities automatically when no annotations are provided
  • Refine layouts for optimal group separation with common graph algorithms
  • Highlight and export publication-quality figures interactively
  • Compare network topology metrics across different datasets
🚀 Key Features
  • Multi-network support: Load and visualize several networks side by side.
  • Annotation overlays:
    • Pie-chart nodes for multi-category annotations
    • Convex-hulls for set-overlap style visualization
  • Community detection: Fast algorithms (e.g., Louvain, Infomap) for de novo grouping.
  • Flexible layouts: Fruchterman–Reingold, Kamada–Kawai, circular, grid, and more.
  • Interactive figure export: Customize colors, sizes, labels; download as PNG or PDF.
  • Topological analysis: Compute degree, clustering coefficient, betweenness, etc., and compare across networks.
🛠 Installation
  1. Install R (≥4.0)
  2. Install RStudio (optional, but recommended)
  3. Clone this repo
    git clone https://github.com/yourusername/NORMA.git
cd NORMA
  4. Install required packages
    # From your R console:
install.packages(c(
"shiny", "igraph", "visNetwork", "plotly",
"data.table", "DT", "RColorBrewer"
))
  5. Run the app
    # In RStudio or R console:shiny::runApp("path/to/NORMA")
💻 Usage
  • Online demo: Launch NORMA in your browser
  • Local: Once the app is running, use the sidebar to upload:
    • Network file (edge list or adjacency)
    • Annotation file (tab-delimited with node → category)
  • Toggle between “Pie-chart nodes” and “Convex-hulls” in Visualization.
  • Explore Layout, Annotation, and Analysis tabs for customization.
📂 Input Formats
  • Network:
    • Edge list: source<TAB>target
    • Adjacency matrix: CSV or TSV
  • Annotations:
    • Plain table:
      node_id<TAB>category1,category2,...

  • See the Help → Input File tab in the app for detailed examples.
📊 Examples & Demo Data
Download sample networks and annotation sets from the app’s Help → Examples tab or directly from our website. These include:
  • Human protein–protein interaction subnetworks
  • GO term enrichment outputs for test datasets
  • Synthetic networks demonstrating overlapping modules
📬 Contact & Support
For questions, issues, or feature requests, please email:
George A. Pavlopoulospavlopoulos@fleming.gr
Or open an issue on GitHub:
https://github.com/yourusername/NORMA/issues
📚 Publications
  • NORMA: The Network Makeup Artist
Koutrouli M., Karatzas E., Papanikolopoulou K., Pavlopoulos G.A.
Genomics, Proteomics & Bioinformatics. 2022 Jun;20(3):578⎼586. Epub 2021 Jun 24.
doi: 10.1016/j.gpb.2021.02.005
PMID: 34171457
  • The network makeup artist (NORMA-2.0): Distinguishing annotated groups in a network using innovative layout strategies
Karatzas E., Koutrouli M., Baltoumas F.A., Papanikolopoulou K., Bouyioukos C., Pavlopoulos G.A.
Bioinformatics Advances. 2022 May 13;2(1):vbac036.
doi: 10.1093/bioadv/vbac036
PMID: 36699373
📄 License
This project is licensed under the MIT License – see the LICENSE file for details.
About
Network annotation visualization
pavlopoulos-lab-services.org/shiny/app/norma
Resources
Readme
MIT license
Activity
Stars
18 stars
Watchers
2 watching
Forks
6 forks
Report repository
Releases
Packages
Contributors
Languages