Quality Report Generation for MaxQuant and mzTab Results [R package PTXQC version 1.1.3]

Chris Bielow

PTXQC: Quality Report Generation for MaxQuant and mzTab Results

Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the MaxQuant software suite (from .txt files) or mzTab files (ideally from OpenMS 'QualityControl' tool). Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format. Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015) <doi:10.1021/acs.jproteome.5b00780>.

Version: 1.1.3

Depends: R (≥ 3.3.0)

Imports: data.table, ggplot2 (≥ 3.4), ggdendro, grid, gridExtra, grDevices, gtable, htmlTable, knitr (≥ 1.10), magrittr, methods, plyr, R6, R6P, RColorBrewer, reshape2, rlang, rmarkdown, rmzqc (≥ 0.5.0), seqinr, stats, utils, UpSetR, xml2, yaml

Suggests: testthat

Published: 2025年07月15日

DOI: 10.32614/CRAN.package.PTXQC

Author: Chris Bielow [aut, cre], Juliane Schmachtenberg [ctb], Swenja Wagner [ctb], Patricia Scheil [ctb], Tom Waschischek [ctb], Guido Mastrobuoni [dtc, rev]

Maintainer: Chris Bielow <chris.bielow at bsc.fu-berlin.de>

BugReports: https://github.com/cbielow/PTXQC/issues

License: BSD_3_clause + file LICENSE

URL: https://github.com/cbielow/PTXQC

NeedsCompilation: no

SystemRequirements: pandoc (http://pandoc.org) for building Vignettes and output reports as HTML

Citation: PTXQC citation info

Materials: README, NEWS

In views: Omics

CRAN checks: PTXQC results

Documentation:

Reference manual: PTXQC.html , PTXQC.pdf

Vignettes: Basic R-Usage Guide for PTXQC (source, R code)
Customizing PTXQC reports (source)
Drag'n'drop Usage Guide for PTXQC (source)
Frequently asked questions for PTXQC (source)
Input/Output data for PTXQC (source, R code)
List of Metrics (source, R code)

Downloads:

Package source: PTXQC_1.1.3.tar.gz

Windows binaries: r-devel: PTXQC_1.1.3.zip, r-release: PTXQC_1.1.3.zip, r-oldrel: PTXQC_1.1.3.zip

macOS binaries: r-release (arm64): PTXQC_1.1.3.tgz, r-oldrel (arm64): PTXQC_1.1.3.tgz, r-release (x86_64): PTXQC_1.1.3.tgz, r-oldrel (x86_64): PTXQC_1.1.3.tgz

Old sources: PTXQC archive

Reverse dependencies:

Reverse imports: RKorAPClient

Linking:

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