Prostar is a software tool devoted to the processing of label-free relative quantitative proteomics data produced by bottom-up LC-MS/MS experiments. Built on R biostatistics routines and web-based graphical user interfaces (Shiny technology), it is free, open-source and distributed via the BioConductor initiative. It is suited to a large type of users, ranging from occasional (with the stand-alone versions) to systematic use on a large proteomics platform (thanks to its server deployment options). It was designed to fit to a large number of quantitative data formats (including MaxQuant and Proline). Prostar contains numerous procedures to preprocess quantitative data, i.e. filtering, normalization, missing value imputation, aggregation of peptide intensities into protein ones, and null hypothesis significance testing. Moreover, it proposes numerous data mining tools, ranging from exploratory statistics to GO analysis, as well as most importantly, tools to select the most likely differentially abundant proteins with a corresponding false discovery rate.

http://www.prostar-proteomics.org/