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Published August 7, 2018 | Version 0.10.0
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pmartR: Quality Control and Statistics for Mass Spectrometry-Based Biological Data

  • 1. Pacific Northwest National Laboratory (
  • 1. Pacific Northwest National Laboratory (



pmartR - An Open-source R package for Statistical Quality Control (QC) of Mass Spectrometry-Based Biological Data

The pmartR package provides a single software tool for QC (filtering and normalization), exploratory data analysis (EDA), and statistical analysis (robust to missing data) and includes numerous visualization capabilities of mass spectrometry (MS) omics data (proteomic, metabolomic, and lipidomic data). The pmartR package provides the necessary capabilities for preparing and performing statistical MS data analysis using simple function calls. Data objects are automatically updated with information about the analysis as it is performed, streamlining the data exploration, QC, and statistical analysis process for the user.

  • Example Data: Example peptide (both unlabeled and isobaric labeled), protein, metabolite and lipid data are available in the pmartRdata package available on Github, and used for illustration purposes in pmartRqc.
  • Parent Repository:
  • Package Requirements: R (>= 3.0.0)


Notes (En)

It's been noted here that there are issues with Rtools for R version 3.5.1.



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Additional details


Modeling Host Responses to Understand Severe Human Virus Infections U19AI106772
National Institutes of Health


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Programming language
R, HTML, C++
Development Status