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Welcome.Rmd
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---
output: html_document
---
# **Welcome!**
### *The KSEA App computationally infers relative kinase activity from quantitative phosphoproteomics data.*
<br><br>
New to this site? For help getting started, read our **User Manual**, found in the left panel (top).
**Note: This app currently supports only human protein analysis.**
*Please cite the following papers if using this app:*
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)
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### *Warnings!*
The KSEA App does not store any of the data once the site is reloaded or disconnected. Please save all the results before exiting!
To conserve server run time, the app disconnects automatically after 10 minutes of inactivity.
For highly sensitive and confidential files, we encourage you to run the KSEA App locally on your computer (see below). Alternatively, R programmers can analyze their data using the [KSEAapp R package](https://cran.r-project.org/web/packages/KSEAapp/index.html); details are in https://github.com/casecpb/KSEAapp.
This tool is only for non-commercial use.
By using the KSEA App, which accesses PhosphoSitePlus data, you agree to abide by these [Terms and Conditions](http://www.phosphosite.org/staticDownloads.action).
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### *Source Code and Local Access*
Our source code, along with instructions for local access, can be found on our Github site: https://github.com/casecpb/KSEA.
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#### Thank you for using the KSEA App!
Any questions? Please email ddw34@case.edu.