Published October 30, 2025
| Version v2
Computational notebook
Open
DEprot: a comprehensive R-package for the analyses of label-free quantitation mass-spectrometry data
Authors/Creators
-
1.
The Netherlands Cancer Institute
-
2.
Oncode Institute
- 3. Mass Spectrometry/Proteomics Facility, Netherlands Cancer Institute, Amsterdam, The Netherlands
-
4.
Amsterdam University Medical Centers
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5.
Eindhoven University of Technology
Description
This repository includes all the codes used for the generation of figures presented in Eickhoff et al., NAR Genomics and Bioinformatics (2026)
Table of contents
The repository contains:
- inpute raw unmputed LFQ-intensities tables - and corresponding metadata info - for both RIME and whole cell proteomics; "source" (zipped) folder
- .Rmd and .html reports of the RIME and proteomics analyses are available, as well as imputation and differential analyses
- results of RIME, whole-cell PROTEOMICS, differential analyses and imputation benchmarking, analyses are zipped in folders labelled with the corresponding name
- renv environments for Linux, MacOS and Windows.
Notes
The DEprot R-package is publicly available as a GitHub repository at https://github.com/sebastian-gregoricchio/DEprot. Additional examples and functionalities for DEprot can be found at the publicly available tutorial and technical web-manual.
Files
Differential_analyses_benchmark.zip
Files
(6.7 GB)
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Additional details
Related works
- Is described by
- Journal article: 10.1093/nargab/lqag015 (DOI)
Funding
- Dutch Cancer Society
- Oncode Institute
Dates
- Updated
-
2026-02Revised version (R1)
Software
- Repository URL
- https://github.com/sebastian-gregoricchio/DEprot
- Programming language
- R
- Development Status
- Active