CoralP
CoralP: Flexible visualization of the human phosphatome - Published in JOSS (2019)
Science Score: 98.0%
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
Found 1 DOI reference(s) in JOSS metadata -
✓Academic publication links
Links to: zenodo.org -
✓Committers with academic emails
3 of 10 committers (30.0%) from academic institutions -
✓Institutional organization owner
Organization phanstiellab has institutional domain (phanstiel-lab.med.unc.edu) -
✓JOSS paper metadata
Published in Journal of Open Source Software
Repository
Flexible visualization of the human phosphatome
Basic Info
Statistics
- Stars: 2
- Watchers: 2
- Forks: 2
- Open Issues: 1
- Releases: 1
Metadata Files
README.md
Overview
http://phanstiel-lab.med.unc.edu/coralp/
CoralP is a user-friendly interactive web application for visualizing both quantitative and qualitative data. Qualitative and quantitative features can be represented in branch colors, node colors, and node sizes. Phosphatases can be organized using the published phosphatome tree or as radial or force directed networks. CoralP is simple to use, well documented, and freely available. It is the first and only dedicated tool for phosphatome visualization and is widely applicable to a variety of data types including those generated from proteomic, genomic, epidemiological, and high-throughput screening experiments.
CoralP builds off a Coral, our tool for human kinome visualization which can be found at http://phanstiel-lab.med.unc.edu/CORAL/.
Web App
The CoralP web app can be found at http://phanstiel-lab.med.unc.edu/coralp/.
Running Locally
The easiest way to use CoralP is via the web app linked above. But you can also run it locally if you wish.
Downloading Code
The first step is to download the code. You can do this with Git:
git clone https://github.com/PhanstielLab/coralp.git
or download and extract a compressed .zip file of the latest revision of the repository from https://github.com/PhanstielLab/coralp/archive/master.zip.
Prerequisites
CoralP uses a number of packages. You can use the following code in R to install any you don't already have:
list.of.packages <- c(
"shiny",
"shinydashboard",
"shinyBS",
"readr",
"rsvg",
"shinyWidgets",
"RColorBrewer",
"svgPanZoom",
"colourpicker",
"DT",
"data.tree",
"jsonlite")
new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[, "Package"])]
if(length(new.packages)) install.packages(new.packages)
Running the App
From R, run the following command:
shiny::runApp("/path/to/coralp")
and it should launch the app in your default web browser.
Credit
CoralP was adapated from Coral in the Phanstiel Lab at UNC by Amit Min and Erika Deoudes. Coral is written in R and relies on the following packages: shiny, shinydashboard, shinyBS, readr, rsvg, shinyWidgets, RColorBrewer. Circle and Force Layouts are written in javascript using the amazing D3 library.
Citation
We are currently preparing a manuscript describing CoralP. CoralP makes use of phylogenetic information and tree plots derived from Chen et al., Science Signaling, 2017.
Contributions
We welcome user feedback and contributions on this software. If you have a question or a problem, the best approach is to report it is through GitHub's issue tracker. If you want to propose a change to the source code, either to fix a bug or make an improvement, use a pull request.
Owner
- Name: The Phanstiel Lab
- Login: PhanstielLab
- Kind: organization
- Website: http://phanstiel-lab.med.unc.edu/
- Repositories: 15
- Profile: https://github.com/PhanstielLab
Code repo for the Phanstiel Lab at UNC
JOSS Publication
CoralP: Flexible visualization of the human phosphatome
Authors
Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC 27599, USA
Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC 27599, USA
Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC 27599, USA
Curriculum in Bioinformatics & Computational Biology, University of North Carolina, Chapel Hill, NC 27599, USA
Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC 27599, USA, Curriculum in Bioinformatics & Computational Biology, University of North Carolina, Chapel Hill, NC 27599, USA, Department of Cell Biology & Physiology, University of North Carolina, Chapel Hill, NC 27599, USA, Lineberger Comprehensive Cancer Research Center, University of North Carolina, Chapel Hill, NC 27599, USA
Editor
Mark A. Jensen
Tags
R shiny D3.js phosphatase phosphatomeGitHub Events
Total
Last Year
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Craig Wenger | c****r@g****m | 33 |
| Amit Min | a****n@l****u | 20 |
| Doug Phanstiel | d****i@s****u | 8 |
| Douglas Phanstiel | d****i@w****u | 5 |
| unknown | a****n@g****m | 3 |
| Erika Deoudes | ed@e****m | 3 |
| Doug Phanstiel | d****i@d****n | 3 |
| Erika Deoudes | e****s@e****n | 2 |
| Eric Davis | e****s@o****m | 1 |
| Doug Phanstiel | d****i@d****t | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 5
- Total pull requests: 0
- Average time to close issues: 1 day
- Average time to close pull requests: N/A
- Total issue authors: 3
- Total pull request authors: 0
- Average comments per issue: 1.2
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- HIM72 (2)
- daissi (2)
- boby-mathew (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- DT * imports
- RColorBrewer * imports
- colourpicker * imports
- data.tree * imports
- jsonlite * imports
- readr * imports
- rsvg * imports
- shiny * imports
- shinyBS * imports
- shinyWidgets * imports
- shinydashboard * imports
- svgPanZoom * imports
- grDevices * suggests
- here * suggests
- shinytest * suggests
- testthat * suggests