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. 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. 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.

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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
3. Hornbeck P.V., et al. (2015) PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Nucleic Acids Res. 43:D512-20
4. Horn H., et al. (2014) KinomeXplorer: an integrated platform for kinome biology studies. Nat Methods. 11(6):603-4

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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.
• Please read and abide by RStudio's Terms of Use.