Statistical tools for quantitative proteomics

Statistical tools for other experiment types

MSstats2 [Link]

Protein quantification in global and targeted, label-free and label-based mass spectrometry-based proteomic experiments. Used to test proteins for differential abundance, quantify proteins in biological samples, and for experimental design. It combines the functionalities of the older version of MSstats and of SRMstats, and is designed for integration with other platforms such as Skyline.

SRMstats [Link]

Protein quantification in label-free & label-based Selected Reaction Monitoring (SRM) experiments. Used to test proteins for differential abundance, quantify proteins in biological samples, and for experimental design.

sparseQuant [Link]

Protein quantification in Selected Reaction Monitoring (SRM) experiments utilizing labeled reference peptides. Used design and analyzed experiments where only a subset of the reference peptides is available.

sSeq [Link]

Detection of differentially expressed gens in RNA-seq experiments with small sample size.

HTSmix [Link]

Interpretation of high-throughput perturbation screens measuring low-dimensional quantitative phenotypes.

BQuant [Link]

Automated Bayesian database-based identification and quantification of metabolites in local regions of Nuclear Magnetic Resonance (NMR) spectra.

MBA [Link]

Automated assignment and assessment of uncertainty of protein backbone Nuclear Magnetic Resonances, for use in structural molecular biology.