MSstatsShiny: R-Shiny graphical user interface (GUI) integrated with the MSstats family of packages.

MSstatsShiny enables versatile, scalable, and reproducible analysis for users with limited programming and statistical backgrounds. It provides a point and click end-to-end analysis pipeline applicable to a wide variety of proteomics experimental types, including data-dependedent acquisitions (DDA) which are label-free or tandem mass tag (TMT)-based, as well as DIA, SRM, and PRM acquisitions, answering question such as relative changes in the abundance of peptides, proteins, or post-translational modifications (PTMs). MSstatsShiny includes easily-accessible documentation to bridge the knowledge gap between aspects of experimental design and methods of statistical analysis. To support reproducible research, the application automatically saves users selections and builds an R script that programmatically recreates the analysis. The scripts can be then used to apply the chosen analysis strategy to large datasets. MSstatsShiny can be installed locally via Github or Bioconductor, or utilized directly on the cloud at www.msstatsshiny.com.

 

Overview and tutorial

Installation/Usage

Online availability: www.msstatsshiny.com

To use the GUI online, simply go to the link above to get started. The online version can only handle smaller datatsets under 250 MB. For larger datasets, please install the application locally.

From Bioconductor: MSstatsShiny link

From GitHub: MSstatsShiny

MSstatsShiny GitHub version: link

More detailed install instructions, including how to install the required dependencies are listed in the GitHub install instructions.

Maintainers

• Devon Kohler,  kohler.d@northeastern.edu