ProteomeExpert: A Docker image based web-server for exploring, modeling, visualizing, and mining large-scale proteomic data sets.
ProteomeExpert is an open-source platform-independent browser-based interface for proteome analytics in R. The application is based on the Shiny package and can be run locally or on a server.
There are two different ways to launch ProteomeExpert (PE):
This way is easier and recommended.
- [1] Install Docker (version >= 17.12.0-ce) Download and install Docker from https://docs.docker.com/install/
- [2] Get and run docker image
docker run -p 80:3838 proteomeexpert/latest#on command line - [3] Open the web browser, go to http://ipOfDockerImageHost/pe2
- [1] download the source code from github
- [2] Install R (v >= 3.2) Download and install R from http://cran.us.r-project.org/
- [3] Install R studio (Optional) Download and install RStudio Desktop from http://rstudio.org/download/desktop
- [4] Install packages in install_packages.R
source(“install_packages.R”)#inside R console - [5]
source(“app.R”)#inside R console
Using either way, users can launch PE in a web browser with the address of the installed PE computer. The detailed help pages of how to use PE are in the launched web page. We provide a demo server at https://proteomic.shinyapps.io/peserver/. This server is single-thread and of low-level hardware, we do recommend users to analyze the data using the demo server with small data sets. An upgraded hardware is necessary, according to the possible computational cost of the data, to reach the potential of PE.
Although ProteomeExpert web-interface can handle quite a few data and analysis tasks, you may prefer to write your own R-code. ProteomeExpert provides a bridge to programming in R(studio) by exporting the functions used for analysis (i.e., you can conduct your analysis using the ProteomeExpert web-interface or by calling ProteomeExpert's functions directly from R-code). For more information about programming with ProteomeExpert see the programming page on the documentation site.
Please use the GitHub issue tracker at https://github.com/lifeinfo/proteomeExpert/issues/new if you have any problems.