posted on 2023-01-09, 14:12authored byDavid
J. Degnan, Kelly G. Stratton, Rachel Richardson, Daniel Claborne, Evan A. Martin, Nathan A. Johnson, Damon Leach, Bobbie-Jo M. Webb-Robertson, Lisa M. Bramer
The pmartR (https://github.com/pmartR/pmartR) package was designed for the quality control (QC) and analysis
of mass spectrometry data, tailored to specific characteristics of
proteomic (isobaric or labeled), metabolomic, and lipidomic data sets.
Since its initial release, the tool has been expanded to address the
needs of its growing userbase and now includes QC and statistics for
nuclear magnetic resonance metabolomic data, and leverages the DESeq2, edgeR, and limma-voom R packages for transcriptomic data analyses. These improvements
have made progress toward a unified omics processing pipeline for
ease of reporting and streamlined statistical purposes. The package’s
statistics and visualization capabilities have also been expanded
by adding support for paired data and by integrating pmartR with the trelliscopejs R package for the quick
creation of trellis displays (https://github.com/hafen/trelliscopejs). Here, we present relevant examples of each of these enhancements
to pmartR and highlight how each new feature benefits
the omics community.