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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:

Please use the canonical form https://CRAN.R-project.org/package=protti to link to this page.

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.
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