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https://github.com/casecpb/KSEA
Kinase-Substrate Enrichment Analysis (KSEA) App
https://github.com/casecpb/KSEA
Last synced: 1 day ago
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Kinase-Substrate Enrichment Analysis (KSEA) App
- Host: GitHub
- URL: https://github.com/casecpb/KSEA
- Owner: casecpb
- License: mit
- Created: 2017-02-11T20:08:43.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2017-05-02T20:46:23.000Z (over 7 years ago)
- Last Synced: 2024-09-23T14:03:28.687Z (about 2 months ago)
- Language: R
- Size: 3.49 MB
- Stars: 7
- Watchers: 1
- Forks: 5
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-proteomics - KSEAapp - R - Kinase substrate enrichment analysis. I would recommend using with a freshly downloaded kinase-substarte database from phosphositeplus - [paper](https://pubmed.ncbi.nlm.nih.gov/28655153/) (8. Kinase Motif/Activity Analysis / Table of Contents)
README
# Welcome to the GitHub account for the KSEA App's online tool!
### You can find the source code and all dependent files here!
- **app.R**: the raw R script behind the KSEA App
- **PSP&NetworKIN_Kinase_Substrate_Dataset_July2016.csv**: the Kinase-Substrate (K-S) dataset that the algorithm uses for identifying the substrates for each kinase
- **Sample Experimental Dataset.csv**: the sample data file input
- **User Manual.pdf**: the user manual containing detailed guidelines for navigating through the interface, interpretation of results, troubleshooting, and local installation.
- **Welcome.Rmd**: the markdown file for the Welcome tab in the KSEA App interface
- **www**: the folder holding the site's logo and favicon
# Instructions for Local Access via GitHub
### IMPORTANT!
If you want to analyze your dataset using the KSEAapp R package, go to our sister site https://github.com/casecpb/KSEAapp/ for more details on installation.
If you want to learn how to run the exact same online interface locally on your computer, continue reading.
**Instructions for local online interface access:**
1. Download and install the R programming software [here](https://www.r-project.org/). We recommend you have version 3.0.3 or newer installed. This app has not been tested on older versions.
2. Download and install the free R Studio software [here](https://www.rstudio.com/products/rstudio/download/). This provides a useful interface for R programming.
(This step is optional; if you choose to skip it, steps 3-6 can be done exactly as described within the R program's basic console.)
3. Open R Studio, and install the Shiny package by typing in the following command into your console, and then hit **Enter**. This may take up to a minute for completion.
```
install.packages("shiny")
```
4. Once the “>” symbol and cursor reappear, type in the following code, and then hit **Enter**.
```
shiny::runGitHub('KSEA', 'casecpb')
```
5. The KSEA App should then automatically launch in a new window/browser tab. This step may take a few seconds.
6. When finished with the analysis, just exit the interface. Then, if needed, hit the escape (Esc) key within the R studio console to terminate the KSEA App. Ignore the warning messages that may appear, and exit from R Studio.
*Note: steps 1-3 only need to be done once if you are using the same computer. If you wish to access the KSEA App again after the first time, just reopen R Studio, and go straight to step 4.*
Instructions can also be found in the User Manual.
-----
Please cite the following papers if using this tool:
1. Wiredja D.D., Koyutürk M., Chance M.R. (2017) The KSEA App: a web-based tool for kinase activity inference from quantitative phosphoproteomics. *Submitted for review*.
2. [Casado, P., et al. (2013) Kinase-substrate enrichment analysis provides insights into the heterogeneity of signaling pathway activation in leukemia cells. *Sci. Signal*. 6, rs6-rs6](http://stke.sciencemag.org/content/6/268/rs6.long)
3. [Hornbeck P.V., et al. (2015) PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. *Nucleic Acids Res*. 43:D512-20](https://academic.oup.com/nar/article/43/D1/D512/2439467/PhosphoSitePlus-2014-mutations-PTMs-and)
4. [Horn H., et al. (2014) KinomeXplorer: an integrated platform for kinome biology studies. *Nat Methods*. 11(6):603-4](http://www.nature.com/nmeth/journal/v11/n6/full/nmeth.2968.html)
-----
Since the KSEA App is hosted on RStudio's shinyapps.io server and accesses PhosphoSitePlus data, the following must be noted:
- This tool is intended for non-commercial use.
- Please read and abide by PhosphoSitePlus's [Terms and Conditions](http://www.phosphosite.org/staticDownloads.action).
- Please read and abide by RStudio's [Terms of Use](https://www.rstudio.com/about/shinyapps-terms-use/).