MSstats
Bioc currentProtein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
Release Lineage
Entered 2.13 · Oct 15, 2013
Current · Requires R 4.6
Description
A set of tools for statistical relative protein significance analysis in DDA, SRM and DIA experiments.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
179 35 exported
Complexity
3.6 avg / 24 max
Call network
179 nodes / 176 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
13,166
Files
217
Compiled share
3.1%
Has compiled src
Yes
Language breakdown
API
Exported functions
45
Internal functions
123
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
4.3%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0
System requirements
–
C++ standard
C++11
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
26
First release
2014-02-04
Latest release
2026-04-28
Avg cadence
185 days
Cold removal rate
100%
Dep drift
54
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 133 (92 internal)
- Examples that run
- 97%35 run in a plain check · 1 never run
- Exported functions with examples
- 83%
- Documented parameters
- 99%
- Return-value docs
- 69%
- Help pages citing references
- 2%
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
4 practices detected in the Bioconductor git repository
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| DDARawData | data.frame | 2,070 × 10 | No other package |
| DDARawData.Skyline | data.frame | 11,934 × 12 | No other package |
| DIARawData | data.frame | 980 × 10 | No other package |
| SRMRawData | data.frame | 720 × 10 | No other package |
| example_SDRF | data.table | 160 × 28 | No other package |
Topics
Depended on by (8)
Bioconductor (8)
Suggested by (3)
People
- Meena Choi author maintainer
- Ting Huang author
- Devon Kohler author
- Deril Raju author
- Mateusz Staniak author
- Tsung-Heng Tsai author
- Olga Vitek author
- Tony Wu author
Cite
Cite this package
Run in R for the authors' entry:
citation("MSstats")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.