Statistical tools for quantitative proteomics

Statistical tools for other experiment types

MSstats is an R package for statistical relative quantification of proteins and peptides in global, targeted and data-independent proteomics. It handles shotgun, label-free and label-based (universal synthetic peptide-based) SRM (selected reaction monitoring), and SWATH/DIA (data independent acquisition) experiments. It can be used for experiments with complex designs (e.g. comparing multiple experimental conditions, or a time course).

MSstats 2.0 supersedes the older version of MSstats and SRMstats, in that it combines and extends the functionalities of these packages, and is designed for integration with other platforms such as Skyline.

SparseQuant is an R package for statistical relative quantification of proteins and peptides in targeted SRM (selected reaction monitoring) proteomic experiments with universal isotope-labeled reference proteins or peptides.

SparseQuant is specifically designed for experiments where only a subset of the reference peptides or proteins are available.

SRMstats is an R package for statistical relative quantification of proteins and peptides in targeted SRM (selected reaction monitoring) proteomic experiments with universal isotope-labeled reference proteins or peptides.

SRMstats is maintained for backward compatibility only. For new features please use MSstats 2.0 above.

sSeq is an R package for detecting differentially expressed gens in RNA-seq experiments with small sample size.

HTSmix is an R package for Interpretation of high-throughput perturbation screens measuring low-dimensional quantitative phenotypes.

BQuant is an R package for automated Bayesian database-based identification and quantification of metabolites in local regions of Nuclear Magnetic Resonance (NMR) spectra.

MBA

MBA is a JAVA tool for automated assignment and assessment of uncertainty of protein backbone Nuclear Magnetic Resonances, for use in structural molecular biology.