KSEAapp

Welcome to the GitHub page for the KSEAapp R Package!

Overview

The KSEAapp R package offers a panel of functions for kinase activity inference on an input phosphoproteomics dataset using the Kinase-Substrate Enrichment Analysis (KSEA) method originally described by Casado et al. (see references below).

For details on its usage and features, please read the Overview.Rmd file within the vignettes folder.

Note: if you are interested in performing KSEA through a user-friendly online interface, please visit this link, or get details from our other GitHub site.

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Page Contents

1. data folder: collection of all the sample datasets in .RData format
2. man folder: collection of documentation files
3. R folder: collection of the raw R functions found within the package
4. vignettes folder: currently contains an Overview.Rmd file that walks readers through the functionality of the package. This is a good starting point for understanding how to use the available functions.
5. DESCRIPTION file
6. LICENSE file
7. NAMESPACE file

Elements found in 2, 5, 6, and 7 are key components for building the R package but are not crucial for understanding the basis of the KSEA calculations.

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Package Installation

There are 2 options for installing the KSEAapp package within the R console:

(1) Via CRAN

This gives access to the newest CRAN release version.

install.packages("KSEAapp")

(2) Via GitHub

This gives access to the newest development version.

install.packages("devtools") # this installs the devtools R package 
devtools::install_github("casecpb/KSEAapp")

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References:

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