Package: ProteoMM Title: Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform Version: 1.25.0 Description: 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). Author: Yuliya V Karpievitch, Tim Stuart and Sufyaan Mohamed Maintainer: Yuliya V Karpievitch <yuliya.k@gmail.com> License: MIT LazyData: TRUE Depends: R (>= 3.5) Encoding: UTF-8 RoxygenNote: 6.1.0 Imports: gdata, biomaRt, ggplot2, ggrepel, gtools, stats, matrixStats, graphics biocViews: ImmunoOncology, MassSpectrometry, Proteomics, Normalization, DifferentialExpression Suggests: BiocStyle, knitr, rmarkdown VignetteBuilder: knitr