- 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
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:
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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.
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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.)
- 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")
- Once the “>” symbol and cursor reappear, type in the following code, and then hit Enter.
shiny::runGitHub('KSEA', 'casecpb')
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The KSEA App should then automatically launch in a new window/browser tab. This step may take a few seconds.
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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:
- 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.
- 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
- Hornbeck P.V., et al. (2015) PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Nucleic Acids Res. 43:D512-20
- Horn H., et al. (2014) KinomeXplorer: an integrated platform for kinome biology studies. Nat Methods. 11(6):603-4
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.