MSstatsShiny
Bioc currentMSstats GUI for Statistical Anaylsis of Proteomics Experiments
Release Lineage
Entered 3.16 · Nov 2, 2022
Current · Requires R 4.6
Description
MSstatsShiny is an R-Shiny graphical user interface (GUI) integrated with the R packages MSstats, MSstatsTMT, and MSstatsPTM. It provides a point and click end-to-end analysis pipeline applicable to a wide variety of experimental designs. These include data-dependedent acquisitions (DDA) which are label-free or tandem mass tag (TMT)-based, as well as DIA, SRM, and PRM acquisitions and those targeting post-translational modifications (PTMs). The application automatically saves users selections and builds an R script that recreates their analysis, supporting reproducible data analysis.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
170 25 exported
Complexity
5.5 avg / 138 max
Call network
170 nodes / 193 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
22,617
Files
143
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
25
Internal functions
147
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
1.15
testthat edition
3
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
2.8%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.2
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
8
First release
2023-03-02
Latest release
2026-04-28
Avg cadence
168 days
Cold removal rate
–
Dep drift
12
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 97%
- Documented parameters
- 96%
- Return-value docs
- 96%
- References docs
- 0%
Topics
People
- Anthony Wu author maintainer
- Meena Choi author
- Ting Huang author
- Maanasa Kaza author
- Devon Kohler author
- Dhaval Mohandas author
- Cristina Pasi author
- Deril Raju author
- Eduard Sabido author
- Mateusz Staniak author
- Olga Vitek author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("MSstatsShiny")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.