ProteoMM: Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform

ProteoMM is a statistical method to perform model-based peptide-level differential expression analysis of single or multiple datasets. For multiple datasets ProteoMM produces a single fold change and p-value for each protein across multiple datasets. ProteoMM provides functionality for normalization, missing value imputation and differential expression. Model-based peptide-level imputation and differential expression analysis component of package follows the analysis described in “A statistical framework for protein quantitation in bottom-up MS based proteomics" (Karpievitch et al. Bioinformatics 2009). EigenMS normalisation is implemented as described in "Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition." (Karpievitch et al. Bioinformatics 2009).

Package details

AuthorYuliya V Karpievitch, Tim Stuart and Sufyaan Mohamed
Bioconductor views DifferentialExpression ImmunoOncology MassSpectrometry Normalization Proteomics
MaintainerYuliya V Karpievitch <[email protected]>
LicenseMIT
Version1.0.1
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ProteoMM")

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ProteoMM documentation built on Jan. 5, 2019, 6:39 p.m.