MSstatsShiny

This repository contains the code for the R Shiny app MSstatsShiny, which utilizes MSstats, MSstatsTMT, and MSstatsPTM to analyze proteomics experiments.

Availability

The application is available both online and locally, via Bioconductor or Github.

Online

The online application is located at http://www.msstatsshiny.com/. The online version is constrained to processing only input files smaller than 100 MB. Due to this, we recommend processing large datasets using a local installation.

Bioconductor

To install the application via Bioconductor, please use the following steps.

1. Download R and RStudio - How to. Note R version must be >= 4.3
2. Intall the package via Bioconductor

Github

To install the application via Github, please use the following steps.

1. Download R and RStudio - How to. Note R version must be >= 4.3
2. Install the package by executing devtools::install_github("Vitek-Lab/MSstatsShiny") in the console.
3. Run the application by executing library(MSstatsShiny) and launch_MSstatsShiny() or MSstatsShiny::launch_MSstatsShiny() in the console.

Citation

To cite this application please use the corresponding publicaiton in the journal of proteome research.

MSstatsShiny: A GUI for Versatile, Scalable, and Reproducible Statistical Analyses of Quantitative Proteomic Experiments

Devon Kohler, Maanasa Kaza, Cristina Pasi, Ting Huang, Mateusz Staniak, Dhaval Mohandas, Eduard Sabido, Meena Choi, and Olga Vitek. Journal of Proteome Research 2023 22 (2), 551-556 DOI: 10.1021/acs.jproteome.2c00603