PTXQC

1.1.5

Quality Report Generation for MaxQuant and mzTab Results

1packages depend

7.1Kdownloads / year

74.8%test coverage

11/13checks pass

Overview

About

Maintained by Chris BielowFirst published 2016-10-1135 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)openSUSE (OBS)

install.packages("PTXQC", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("cbielow/PTXQC")

Development version from cbielow/PTXQC. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-ptxqc

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-PTXQC

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 6.8 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.05

74.8%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-07-11
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,185 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 99%
Return-value docs: 95%
References docs: 0%

Downloads

7.1K

CRAN downloads in the past year

Rank #4,682 · ~19/day · ~591/mo

Releases R versions

Daily download trend is not available in this view yet.

39430 days

1.9K90 days

7.1K1 year

Compare downloads with other packages →

Also on184 r2u22 autocran4.3K conda_forge26 c2d4u

Repository

GitHub ↗ cbielow/ptxqc

47Stars

26Forks

14Open issues

1Open PRs

19Releases

714Commits

10Contributors

maxquantquality-controlreportmetricproteomicsheatmapmatch-between-runsdrag-and-drop

714 commits · Last activity 2026-07-16 · +2.2% stars, 30d

Stars over time

2025-06-04 · 442026-07-07 · 47

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/cbielow/ptxqc on 2026-07-19.

Continuous integration (1)

Travis CI

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.3.0

Imports (24)

data.table ggplot2 ggdendrogridgridExtragrDevicesgtable htmlTable knitr magrittrmethodsplyr R6 R6P RColorBrewer reshape2 rmarkdown rmzqc seqinrstatsutilsUpSetR xml2 yaml

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

RKorAPClient

Code & Tests

People & History

People (6)

Maintainer (1)

Chris Bielow

Author, Maintainer

Authors (1)

Chris Bielow

Author, Maintainer

Contributors (4)

Patricia Scheil

Contributor · added in 1.0.2

Juliane Schmachtenberg

Contributor · added in 1.0.2

Swenja Wagner

Contributor · added in 1.0.2

Tom Waschischek

Contributor · added in 1.0.2

Reviewers (1)

Guido Mastrobuoni

Data contributor, Reviewer · added in 1.0.2

Package Timeline

35 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.1.5Latest
2026-04-23 · current release · diff ↗
1.1.4
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1.1.3
2025-07-15 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.1.2
2025-01-09 · diff ↗
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R 4.4.0 released · 2024-04-24
1.1.1
2024-03-11 · diff ↗
1.1.0
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1.0.17
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1.0.16
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1.0.15
2023-04-25 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.0.14
2022-09-20 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.13
2022-03-22 · diff ↗

Show 32 earlier events

1.0.12
2021-11-04 · diff ↗
1.0.11
2021-10-04 · diff ↗
1.0.10
2021-06-02 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0.9
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1.0.8
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1.0.7
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1.0.5
2020-06-09 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.0.4
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1.0.2
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1.0.1
2020-02-02 · diff ↗
unarchivedReturned to CRAN
2020-02-02
archivedRemoved from CRAN
2020-01-28
check problems were not corrected in time
1.0.0
2020-01-14 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.92.6
2019-04-16 · diff ↗
0.92.5
2019-03-15 · diff ↗
0.92.4
2019-02-08 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.92.3
2018-02-07 · diff ↗
0.92.0
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0.91.0
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0.90.0
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0.82.6
2017-06-09 · diff ↗
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2017-05-04 · diff ↗
R
R 3.4.0 released · 2017-04-21
0.82.3
2017-04-03 · diff ↗
0.82.2
2017-02-17 · diff ↗
0.80.14
2016-10-14 · diff ↗
0.80.13
2016-10-11
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-10-11
Total releases: 35 / 10 yrs
License: BSD_3_clause + file LICENSE OSI
Minimum R: ≥ 3.3.0
Download size: 3.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

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