This repository contains the code for the R Shiny app MSstatsShiny, which utilizes MSstats and MSstatsTMT to analyze proteomics experiments.
The application is available both online and locally.
The online application is located at http://www.msstatsshiny.com/. The online version is constrained by the processing limits of the server. Due to this we recommend only processing small datasets on the platform. Large datasets will likely run out of memory on the data summarization step.
For large file processing, it is recommened you use a local install of the application. To install and run the application locally, please follow these steps.
- Download R and RStudio - How to.
- Download this github repository to your local machine.
- Open RStudio and set working directory to the local repository.
- Install the dependencies listed below.
- Run the application by executing
library(shiny)andrunApp()in the console.
install.packages(c('shiny', 'shinyBS', 'shinybusy', 'shinyjs', 'uuid', 'DT', 'knitr', 'plotly', 'ggrepel', 'gplots', 'tidyverse', 'data.table', 'BiocManager'))
BiocManager::install(c('MSstatsTMT', 'biomaRt'))
Instructions for processing your dataset are listed directly in the application. The general workflow includes: uploading your data into the application, run level summarization and vizualization, and data modeling to determine differential proteins. For questions on how to process your data please see the Help section of the application.