README.md

In gaelfortin/phosphogo: Analyze Your Phosphoproteomic Data

phosphogo

phosphogo is a set of tools to analyze phosphoproteomic data from mouse and human experiments. Kinase-substrate predictions can be performed using NetworKIN and IV-KEA (in vitro kinase enrichment analysis). Databases used by phosphogo are located in the phosphogodb package.

This version of phosphogo does not support R > 4.

Installation

phosphogo can be installed with:

devtools::install_github('wleepang/shiny-directory-input') #dependency for Shiny app
devtools::install_github('gaelfortin/phosphogo')
devtools::install_github('gaelfortin/phosphogodb') #databases required for phosphogo

That's it! You can now use phosphogo in application mode or in command-line mode.

Then, on RStudio, run the following commands:

library(phosphogo)
dir.create('myexperiment/', showWarnings = FALSE)

You are ready to perform all analyses included in phosphogo!

User-friendly application

Phosphogo comes with a intuitive user interface that offers the same functions than the command-line version of the package. To launch the app, run:

library(phosphogo)
phosphogoApp()

You can find demonstration files in the GitHub repository of phosphogo.

Command-line version of phosphogo

Pipeline example

An example of a pipeline can be found in the vignette with the command utils::browseVignettes('phosphogo').

How does phosphogo make kinase-substrate predictions?

Phosphogo relies on the following prediction strategies. Please cite their corresponding authors.

NetworKIN

Horn et al., KinomeXplorer: an integrated platform for kinome biology studies. Nature Methods 2014 Jun;11(6):603–4.

IV-KEA

Phosphogo uses the in vitro database published in: Sugiyama et al., Large-scale Discovery of Substrates of the Human Kinome. Scientific Reports 2019

Issues

If you have an issue or find a bug, please open an issue in the Issues section of the Github repository.

Licence

phosphogo is distributed under the CC BY-NC-SA licence.

Other informations

This package is maintained by Gael Fortin ([e-mail]) and was written on R 3.6.3

gaelfortin/phosphogo documentation built on Nov. 26, 2020, 9:12 a.m.