Package: PTXQC
Type: Package
Title: Quality Report Generation for MaxQuant and mzTab Results
Version: 1.1.5
Date: 2026-04-20
Authors@R: c(person(given = "Chris",
                      family = "Bielow",
                      role = c("aut", "cre"),
                      email = "chris.bielow@bsc.fu-berlin.de"),
               person(given = "Juliane",
                      family = "Schmachtenberg",
                      role = "ctb"),
               person(given = "Swenja",
                      family = "Wagner",
                      role = "ctb"),
               person(given = "Patricia",
                      family = "Scheil",
                      role = "ctb"),
               person(given = "Tom",
                      family = "Waschischek",
                      role = "ctb"),
               person(given = "Guido",
                      family = "Mastrobuoni",
                      role = c("dtc", "rev")))
Description: 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>.
SystemRequirements: pandoc (http://pandoc.org) for building Vignettes
        and output reports as HTML
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, rmarkdown,
        rmzqc (>= 0.5.0), seqinr, stats, utils, UpSetR, xml2, yaml
Suggests: testthat
VignetteBuilder: knitr
License: BSD_3_clause + file LICENSE
Encoding: UTF-8
Roxygen: list()
RoxygenNote: 7.3.2
URL: https://github.com/cbielow/PTXQC
BugReports: https://github.com/cbielow/PTXQC/issues
Config/pak/sysreqs: cmake make libicu-dev libuv1-dev libxml2-dev
        libssl-dev libnode-dev zlib1g-dev
Repository: https://cbielow.r-universe.dev
Date/Publication: 2026-04-23 13:34:42 UTC
RemoteUrl: https://github.com/cbielow/ptxqc
RemoteRef: HEAD
RemoteSha: 74d48b81b744547c53b2fc383704c141ec176df5
NeedsCompilation: no
Packaged: 2026-06-22 10:31:53 UTC; root
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@bsc.fu-berlin.de>