Software

I have developed open-source R/Bioconductor software packages. Check my GitHub page and in particular the MetCirc, MetNet, MatrixQCvis, and MsQuality repositories to learn more about the packages I developed.

I am also the author of the first version pRolocGUI package that was created during an ERASMUS placement at the Computational Proteomics Unit headed by Laurent Gatto (now at UCLouvain) at the University of Cambridge.

Naake T., Rainer J. MsQuality - Quality metric calculation from Spectra and MsExperiment objects. 2023; https://doi.org/10.18129/B9.bioc.MsQuality

Naake T., Huber W. Shiny-based interactive data-quality exploration for omics data. 2023; https://doi.org/10.18129/B9.bioc.MatrixQCvis

Naake T., Salzer L. MetNet: Inferring metabolic networks from untargeted high-resolution mass spectrometry data. 2023; https://doi.org/10.18129/B9.bioc.MetNet.

Naake T., Gaquerel E. MetCirc: Navigating mass spectral similarity in high-resolution MS/MS metabolomics data. 2023; https://doi.org/10.18129/B9.bioc.MetCirc

Breckels L., Naake T., Gatto L. pRolocGUI: Interactive visualisation of spatial proteomics data. 2023; https://doi.org/10.18129/B9.bioc.pRolocGUI