mzR
Bioc currentparser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)
Release Lineage
Entered 2.9 · Nov 1, 2011
Current · Requires R 4.6
Description
mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a subset of the proteowizard library for mzXML, mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
30337 5 exported
Complexity
3 avg / 13 max
Call network
30337 nodes / 43726 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
1,142,456
Files
5,809
Compiled share
99.8%
Has compiled src
Yes
Language breakdown
API
Exported functions
5
Internal functions
26
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.01
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
42.9%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0.0
System requirements
2 externalC++11, GNU make
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
25
First release
2011-11-17
Latest release
2026-04-28
Avg cadence
189 days
Cold removal rate
–
Dep drift
4
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 8
- Examples that run
- 100%7 run in a plain check
- Exported functions with examples
- 75%
- Documented parameters
- 83%
- Return-value docs
- 0%
- Help pages citing references
- 13%
Repository practices
5 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/sneumann/mzr on 2026-10-11.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
Topics
Depended on by (21)
Show all 42 packagesHide all 42 packages
Bioconductor (21)
Suggested by (21)
People
- Steffen Neumann author maintainer
- Laurent Gatto author
- Qiakng Kou author
- Sascha Manier contributor
- Johannes Rainer author
- David Rauh contributor
- Adriano Rutz contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("mzR")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1038/nbt.2377, 10.1074/mcp.r110.000133, 10.1038/nbt1031, 10.1093/bioinformatics/btn323.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.