Northeastern University

College of Science
College of Computer and Information Science
360 Huntington Ave.
Boston, Massachusetts 02115

MSstats

msstatsMSstats is an R package for statistical relative quantification of proteins and peptides in mass spectrometry-based proteomics. It supports label-free and label-based experimental workflows and data-dependent, targeted and data-independent spectral acquisition. It takes as input identified and quantified spectral peaks, and outputs a list of differentially abundant peptides or proteins, or summaries of peptide or protein relative abundance. MSstats relies on a flexible family of linear mixed models.
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Cardinal

cardinal-partial1Cardinal is an R package designed for efficient analysis of mass spectrometry-based imaging experiments. The capabilities include visualization of single and composit ion images, pre-processing (normalization, smoothing, baseline reduction, peak picking, filtering and alignment), as well as traditional and novel supervised and unsupervised methods such as image segmentation (clustering), principle components analysis, and partial least squares discriminant analysis.
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SparseQuant

sparse-quantSparseQuant is an R package for statistical relative quantification of proteins and peptides in targeted proteomic experiments with universal isotope-labeled reference proteins or peptides. SparseQuant is designed for experiments where only a subset of the reference peptides or proteins are available. We plan to merge SparseQuant with MSstats in a near future.
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