The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

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: 0.8.0
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, scales, farver, ggforce
Published: 2024-03-28
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
Single Dose Treatment Data Analysis Workflow
Input Preparation Workflow
Protein Structure Analysis Workflow
Qualtiy Control (QC) workflow

Downloads:

Package source: protti_0.8.0.tar.gz
Windows binaries: r-devel: protti_0.8.0.zip, r-release: protti_0.8.0.zip, r-oldrel: protti_0.8.0.zip
macOS binaries: r-release (arm64): protti_0.8.0.tgz, r-oldrel (arm64): protti_0.8.0.tgz, r-release (x86_64): protti_0.8.0.tgz, r-oldrel (x86_64): protti_0.8.0.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.
Health stats visible at Monitor.