pmartR
Provides functionality for quality control processing and statistical analysis of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level), lipidomic, and metabolomic data, as well as RNA-seq based count data and nuclear magnetic resonance (NMR) data. This includes data transformation, specification of groups that are to be compared against each other, filtering of features and/or samples, data normalization, data summarization (correlation, PCA), and statistical comparisons between defined groups. Implements methods described in: Webb-Robertson et al. (2014) <doi:10.1074/mcp.M113.030932>. Webb-Robertson et al. (2011) <doi:10.1002/pmic.201100078>. Matzke et al. (2011) <doi:10.1093/bioinformatics/btr479>. Matzke et al. (2013) <doi:10.1002/pmic.201200269>. Polpitiya et al. (2008) <doi:10.1093/bioinformatics/btn217>. Webb-Robertson et al. (2010) <doi:10.1021/pr1005247>.
- A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label‐free LC ‐ MS proteomics experiments
- A statistical selection strategy for normalization procedures in LC‐MS proteomics experiments through dataset‐dependent ranking of normalization scaling factors
- Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements
- Combined Statistical Analyses of Peptide Intensities and Peptide Occurrences Improves Identification of Significant Peptides from MS-Based Proteomics Data
- DAnTE: a statistical tool for quantitative analysis of -omics data
- Improved quality control processing of peptide-centric LC-MS proteomics data
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