R Observatory: Metrics for PTXQC version 1.1.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PTXQC

1.1.6Package record

Quality Report Generation for MaxQuant and mzTab Results

0packages depend

6.4Kdownloads / year

75.1%test coverage

13/13flavors OK

Overview

About

Maintained by Chris BielowCRAN page ↗GitHub ↗Issues ↗

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)Fedora (COPR)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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-PTXQC

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# 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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 5.9 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-26
NOTE12 OK, 1 NOTE2026-07-11
OK13 OK2026-06-09

Show 3 earlier changesHide 3 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.6

READMEYes · 1,185 wordsVignettesYes · 6 · dynamicNEWSYes · 33% structuredCitation fileYes · cites a publication

Help pages: 119includes a package overview page
Examples that run: 100%55 run in a plain check
Exported functions with examples: 71%
Documented parameters: 99%
Return-value docs: 95%
Help pages citing references: 0%

Vignettes (6)

How these are measured

Downloads

6.4K

CRAN downloads in the past year

Rank #5,807 · ~18/day · ~536/mo

Releases R versions

Daily download trend is not available in this view yet.

51930 days

1.4K90 days

6.4K1 year

Compare downloads with other packages →

Also on173 r2u1 autocran3.7K conda_forge69 c2d4u

How downloads are counted

Repository

cbielow/ptxqc ↗Account: cbielow

48Stars

26Forks

14Open issues

1Open PRs

19Releases

720Commits

10Commit identities

maxquantquality-controlreportmetricproteomicsheatmapmatch-between-runsdrag-and-drop

720 commits · Last activity 2026-08-23 · 0% stars, 30d · Discussions: 1 post

Responsiveness

How these are sampled

PRs merged (all time): 88%
Median days to close, 50 most recently updated closed issues: 2
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-10-21 · 462026-09-02 · 48

How these are measured

PracticesBeta

4 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/cbielow/ptxqc on 2026-10-18.

Continuous integration (1)

Travis CI (config file)

Governance and community (2)

Code of conductContributing guide

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Installing PTXQC adds 90 packages (46 with compiled code, 77 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

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

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (6)

Chris Bielow

Author, Maintainer since 0.80.13 (2016)

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

Guido Mastrobuoni

Data contributor, Reviewer · added in 1.0.2

Releases (36)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.1.6Latest
record
2026-04-23 · current release · diff ↗
1.1.5
record
2026-04-23 · diff ↗
1.1.4
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2026-02-18 · diff ↗
1.1.3
record
2025-07-15 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.1.2
record
2025-01-09 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.1.1
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2024-03-11 · diff ↗
1.1.0
record
2023-12-15 · diff ↗ ·
added 3 exports
modsToTable, modsToTableByRaw, plot_peptideMods
1.0.17
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2023-07-11 · diff ↗
1.0.16
record
2023-05-17 · diff ↗
1.0.15
record
2023-04-25 · diff ↗ ·
removed 19 exports
CVDictionarySingleton, MzQCDateTime, MzQCanalysisSoftware, MzQCbaseQuality, MzQCcontrolledVocabulary, MzQCcvParameter, MzQCinputFile, MzQCmetadata, MzQCmzQC, MzQCqualityMetric, NULL_to_NA, NULL_to_charNA, fromDatatoMzQC, getCVDictionary, hasFileSuffix, isUndefined, isValidMzQC, removeSuffix, suffixToCV
R
R 4.3.0 released · 2023-04-21
1.0.14
record
2022-09-20 · diff ↗ ·
added 1 export
plot_DataOverRT
R
R 4.2.0 released · 2022-04-22

Show 33 earlier eventsHide 33 earlier events

1.0.13
record
2022-03-22 · diff ↗
1.0.12
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2021-11-04 · diff ↗
1.0.11
record
2021-10-04 · diff ↗ ·
removed 1 export
parseOBO

added 7 exports
CVDictionarySingleton, QCMetaFilenames, assembleMZQC, getCVDictionary, hasFileSuffix, removeSuffix, suffixToCV
1.0.10
record
2021-06-02 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0.9
record
2021-02-03 · diff ↗ ·
removed 1 export
addGGtitle

added 15 exports
MzQCDateTime, MzQCanalysisSoftware, MzQCbaseQuality, MzQCcontrolledVocabulary, MzQCcvParameter, MzQCinputFile, MzQCmetadata, MzQCmzQC, MzQCqualityMetric, NULL_to_NA, NULL_to_charNA, fromDatatoMzQC, isUndefined, isValidMzQC, parseOBO
1.0.8
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2020-12-13 · diff ↗
1.0.7
record
2020-11-12 · diff ↗ ·
added 1 export
createYaml
1.0.5
record
2020-06-09 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.0.4
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2020-03-28 · diff ↗
1.0.2
record
2020-02-11 · diff ↗
unarchivedReturned to CRAN
2020-02-02
1.0.1
record
2020-02-02 · diff ↗
archivedRemoved from CRAN
2020-01-28
check problems were not corrected in time
1.0.0
record
2020-01-14 · diff ↗ ·
added 2 exports
FilenameMapper, plot_TIC
R
R 3.6.0 released · 2019-04-26
0.92.6
record
2019-04-16 · diff ↗
0.92.5
record
2019-03-15 · diff ↗
0.92.4
record
2019-02-08 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.92.3
record
2018-02-07 · diff ↗
0.92.0
record
2017-10-14 · diff ↗
0.91.0
record
2017-10-06 · diff ↗
0.90.0
record
2017-08-05 · diff ↗ ·
added 1 export
getHTMLTable
0.82.6
record
2017-06-09 · diff ↗
0.82.5
record
2017-05-04 · diff ↗
R
R 3.4.0 released · 2017-04-21
0.82.3
record
2017-04-03 · diff ↗
0.82.2
record
2017-02-17 · diff ↗
0.80.14
record
2016-10-14 · diff ↗
0.80.13
record
2016-10-11
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-10-11
Total releases: 36 / 10 yrs
License: BSD_3_clause + file LICENSE OSI · relicensed from GPL-2 in 1.0.2
Minimum R: ≥ 3.3.0
Download size: 3.4 MB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("PTXQC")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1021/acs.jproteome.5b00780.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for PTXQC version 1.1.6 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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