MSnbase
Bioc currentBase Functions and Classes for Mass Spectrometry and Proteomics
Release Lineage
Entered 2.8 · Apr 14, 2011
Current · Requires R 4.6
Description
MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
332 88 exported
Complexity
4.2 avg / 52 max
Call network
332 nodes / 236 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
42,141
Files
316
Compiled share
2.7%
Has compiled src
Yes
Language breakdown
API
Exported functions
92
Internal functions
211
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.42
testthat edition
–
Docs
Roxygen coverage
98.9%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
15.8%
Unsafe pattern score
3
Dep constraint coverage
34.6%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
31
First release
2011-09-20
Latest release
2026-08-07
Avg cadence
179 days
Cold removal rate
100%
Dep drift
31
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 96 (1 internal)
- Examples that run
- 96%80 run in a plain check · 3 never run
- Exported functions with examples
- 83%
- Documented parameters
- 96%
- Return-value docs
- 65%
- Help pages citing references
- 17%
Repository practices
8 development-tooling and community-health practices detected across 5 families in the upstream repository
Checks run against github.com/lgatto/msnbase on 2026-10-18.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2026-10-02 · The repository has a site deploy workflow
pkgdown site last built 2026-10-02
Show all practicesHide 1 practice
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| M | – | – | – |
| M2 | – | – | – |
| TMT10 | – | – | – |
| TMT10ETD | – | – | – |
| TMT10HCD | – | – | – |
| TMT11 | – | – | – |
| TMT11HCD | – | – | – |
| TMT16 | – | – | – |
| TMT16HCD | – | – | – |
| TMT6 | – | – | – |
| TMT6b | – | – | – |
| TMT6plexPurityCorrections | data.frame | 6 × 7 | No other package |
| TMT7 | – | – | – |
| TMT7b | – | – | – |
| iTRAQ4 | – | – | – |
| iTRAQ4plexPurityCorrections | data.frame | 4 × 5 | No other package |
| iTRAQ5 | – | – | – |
| iTRAQ8 | – | – | – |
| iTRAQ8plexPurityCorrections | data.frame | 8 × 9 | No other package |
| iTRAQ9 | – | – | – |
| ipqf1 | – | – | – |
| ipqf2 | – | – | – |
| ipqf3 | – | – | – |
| ipqf4 | – | – | – |
| ipqf5 | – | – | – |
| itraqdata | – | – | – |
| msnset | – | – | – |
| msnset2 | – | – | – |
| msx | – | – | – |
| msx0 | – | – | – |
| naset | – | – | – |
Topics
Depended on by (38)
Show 48 packagesHide 48 packages
Bioconductor (38)
People
- Laurent Gatto author maintainer
- Sebastian Gibb author maintainer
- Johannes Rainer author maintainer
- Lieven Clement contributor
- Miguel Cosenza-Contreras contributor
- Richie Cotton contributor
- Martina Fischer contributor
- Ludger Goeminne contributor
- Vasile-Cosmin Lazar contributor
- Pascal Maas contributor
- Thomas Naake contributor
- Steffen Neumann contributor
- Vladislav Petyuk contributor
- Sigurdur Smarason contributor
- Arne Smits contributor
- Adriaan Sticker contributor
- Samuel Wieczorek contributor
- Guangchuang Yu contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("MSnbase")The package provides a citation file, so citation() returns the authors' own entry.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.