https://github.com/cytoscape/network-ptm-integration
This repo tracks the work of data-driven addition of phosphorylation sites to proteins in networks (and pathways).
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
2 of 3 committers (66.7%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.2%) to scientific vocabulary
Repository
This repo tracks the work of data-driven addition of phosphorylation sites to proteins in networks (and pathways).
Basic Info
- Host: GitHub
- Owner: cytoscape
- License: mit
- Language: R
- Default Branch: main
- Size: 119 MB
Statistics
- Stars: 0
- Watchers: 12
- Forks: 0
- Open Issues: 7
- Releases: 0
Metadata Files
README.md
network-ptm-integration
This repo tracks the work of integrating networks (pathway models) with ptm data. This includes data-driven visualization of phosphorylation sites on proteins in networks, visualization of phosphoproteomics data on manually curated phosphorylation sites, and utility scripts for related tasks.
The RShiny tool is designed as an interactive tool where users can visualize data on relevant phospho sites on pathways. Phospho sites can be visualized in multiple ways: an oval PTM node offset from the parent node for each phospho site, or as a pie chart offset from the node visualizing all phospho sites. The user can choose to visualize all sites in the data, or restrict the sites added based on various methods/data (relevant kinases/phosphatase on the pathway, pan-cancer PROGENy data, inhibitor data).
How to use addptmsites.R
This app is designed to:
- Import and preprocess data: Load phosphoproteomics, proteomics, PROGENy, kinase–substrate, and BioMart mapping files.
- Connect to Cytoscape: Ensure Cytoscape is running, and use RCy3 to import pathways and update network layouts.
- Visualize PTM data, two visualization modes:
- Traditional PTM: Places up to four PTM nodes around each parent protein node.
- Pie Chart: Creates one pie chart visualization of multiple phospho sites per parent protein node.
Prerequisites
Install Cytoscape. (See https://cytoscape.org/download.html) Install R Studio. (See https://posit.co/download/rstudio-desktop/)
Run App
- Launch Cytoscape on your local machine.
- Then launch the Shiny App:
- Run the R script containing the app code in R or RStudio.
* The app will open in your default web browser.
Other scripts
BasicDataViz_ManualAnnotationPTM.R
Example script showing how to do data visualization of proteomics and phosphoproteomics on WikiPathways with manually annotated PTM sites.
ExtractWP-PTMinfo.R
Extract all manually annotated PTMs in WikiPathways.
Owner
- Name: Cytoscape Consortium
- Login: cytoscape
- Kind: organization
- Website: http://www.cytoscape.org/
- Repositories: 153
- Profile: https://github.com/cytoscape
GitHub Events
Total
- Issues event: 10
- Issue comment event: 7
- Push event: 45
Last Year
- Issues event: 10
- Issue comment event: 7
- Push event: 45
Committers
Last synced: 11 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| khanspers | k****s@g****u | 81 |
| yihangx | y****n@g****u | 4 |
| Yihang Xin | 4****x | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 1
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 1
- Total pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- khanspers (9)
- AlexanderPico (3)