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protti: Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

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: 0.9.1
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, scales, farver, ggforce, xml2, jsonlite
Published: 2024-10-21
DOI: 10.32614/CRAN.package.protti
Author: Jan-Philipp Quast ORCID iD [aut, cre], Dina Schuster ORCID iD [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

Documentation:

Reference manual: protti.pdf
Vignettes: Dose-Response Data Analysis Workflow (source, R code)
Single Dose Treatment Data Analysis Workflow (source, R code)
Input Preparation Workflow (source, R code)
Protein Structure Analysis Workflow (source, R code)
Qualtiy Control (QC) workflow (source, R code)

Downloads:

Package source: protti_0.9.1.tar.gz
Windows binaries: r-devel: protti_0.9.1.zip, r-release: protti_0.9.1.zip, r-oldrel: protti_0.9.1.zip
macOS binaries: r-release (arm64): protti_0.9.1.tgz, r-oldrel (arm64): protti_0.9.1.tgz, r-release (x86_64): protti_0.9.1.tgz, r-oldrel (x86_64): protti_0.9.1.tgz
Old sources: protti archive

Linking:

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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.