Useful functions and workflows for proteomics quality control and data analysis of both limited proteolysis-coupled mass spectrometry (LiP-MS) (Feng et. al. (2014) <doi:10.1038/nbt.2999>) and regular bottom-up proteomics experiments. Data generated with search tools such as 'Spectronaut', 'MaxQuant' and 'Proteome Discover' can be easily used due to flexibility of functions.
| Version: |
0.6.0 |
| Depends: |
R (≥ 4.0) |
| Imports: |
rlang, dplyr, stringr, magrittr, data.table, janitor, progress, purrr, tidyr, ggplot2, forcats, tibble, plotly, ggrepel, utils, grDevices, curl, readr, lifecycle, httr, methods, R.utils, stats |
| Suggests: |
testthat, covr, knitr, rmarkdown, shiny, r3dmol, proDA, limma, dendextend, pheatmap, heatmaply, furrr, future, parallel, seriation, drc, igraph, stringi, STRINGdb, iq |
| Published: |
2023-01-20 |
| Author: |
Jan-Philipp Quast 
[aut, cre],
Dina Schuster
[aut],
ETH Zurich [cph, fnd] |
| Maintainer: |
Jan-Philipp Quast <quast at imsb.biol.ethz.ch> |
| BugReports: |
https://github.com/jpquast/protti/issues |
| License: |
MIT + file LICENSE |
| URL: |
https://github.com/jpquast/protti,
https://jpquast.github.io/protti/ |
| NeedsCompilation: |
no |
| Citation: |
protti citation info |
| Materials: |
README NEWS |
| In views: |
Omics |
| CRAN checks: |
protti results |