The Journal of Open Source Software · 2023 · 60 citations · 9 references
Life SciencesBioinformaticsBiostatisticsMass Spectrometric AnalysisProteomicsProteomics InformaticsBottom-up ProteomicsMass SpectrometryMass Spectrometry Data AnalysisMass Spectrometry-based ProteomicsQuantitative ProteomicsData AnnotationDifferential Abundance AnalysisProtein Abundance AnalysisProtein AnnotationProtein Mass SpectrometryProteomic Data AnalysisQuantitative Proteomics WorkflowsStatistical Experimental Design
proteoDA is an R package designed to analyze high resolution intensity-based mass spectrometry data.proteoDA was designed to be streamlined and user-friendly.proteoDA is built around a DAList, a custom R class, which is used to hold the data, statistical design, and results for a differential abundance analysis.Users import protein abundance data, protein annotation data, and sample metadata into a DAList, and all further functions operate on that list.Once the data are in DAList, proteoDA provides functions for further steps of the analysis Figure 1.
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The ProteomeXchange consortium at 10 years: 2023 update
Eric W. Deutsch, Nuno Bandeira, Yasset Pérez‐Riverol et al. · Nucleic Acids Research · 2022 · 865 citations · Full text
Glimma: interactive graphics for gene expression analysis
Shian Su, Charity W. Law, Casey Ah-Cann et al. · Bioinformatics · 2017 · 219 citations · Full text