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The 'Proteomics Eye' ('ProtE') offers a comprehensive and intuitive framework for the univariate analysis of label-free proteomics data. By integrating essential data wrangling and processing steps into a single function, 'ProtE' streamlines pairwise statistical comparisons for categorical variables. It provides quality checks and generates publication-ready visualizations, enabling efficient and robust data analysis. 'ProtE' is compatible with proteomics data outputs from 'MaxQuant' (Cox & Mann, (2008) <doi:10.1038/nbt.1511>), 'DIA-NN' (Demichev et al., (2020) <doi:10.1038/s41592-019-0638-x>), and 'Proteome Discoverer' (Thermo Fisher Scientific, version 2.5). The package leverages 'ggplot2' for visualization (Wickham, (2016) <doi:10.1007/978-3-319-24277-4>) and 'limma' for statistical analysis (Ritchie et al., (2015) <doi:10.1093/nar/gkv007>).
| Version: | 1.0.1 |
| Depends: | R (≥ 2.10) |
| Imports: | dplyr, circlize, vegan, UniProt.ws, stringr, missRanger, vsn, car, openxlsx, tidyr, broom, reshape2, ggpubr, ggplot2, VIM, forcats, grDevices, grid, limma, ComplexHeatmap |
| Suggests: | BiocManager, rmarkdown, knitr |
| Published: | 2025-01-15 |
| DOI: | 10.32614/CRAN.package.ProtE |
| Author: | Theodoros Margelos [aut, cre, cph], Rafael Stroggilos [ctb, cph] |
| Maintainer: | Theodoros Margelos <ted.margelos02 at gmail.com> |
| BugReports: | https://github.com/theomargel/ProtE/issues |
| License: | MIT + file LICENSE |
| URL: | https://github.com/theomargel/ProtE |
| NeedsCompilation: | no |
| Language: | en-US |
| Materials: | README NEWS |
| CRAN checks: | ProtE results |
| Reference manual: | ProtE.pdf |
| Vignettes: |
ProtE Workflow (source) Introduction to ProtE (source, R code) |
| Package source: | ProtE_1.0.1.tar.gz |
| Windows binaries: | r-devel: ProtE_1.0.1.zip, r-release: ProtE_1.0.1.zip, r-oldrel: ProtE_1.0.1.zip |
| macOS binaries: | r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.