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.
None published for Bioconductor
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
140
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
25
Internal functions
147
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
1.15
testthat edition
3
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
- Help pages
- 43 (1 internal)includes a package overview page
- Examples that run
- 97%37 run in a plain check · 1 never run
- Exported functions with examples
- 96%
- Documented parameters
- 96%
- Return-value docs
- 96%
- Help pages citing references
- 0%
Repository practices
3 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/vitek-lab/msstatsshiny on 2026-10-22.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| annotation | data.frame | 10 × 3 | No other package |
| annotation.mine | data.frame | 72 × 7 | 2 packages |
| annotation.mq | data.frame | 150 × 7 | 2 packages |
| annotation.pd | data.frame | 150 × 7 | 2 packages |
| dataset | data.frame | 6,390 × 11 | No other package |
| dia_skyline_model | list | 3 elements | No other package |
| dia_skyline_summarized | list | 3 elements | No other package |
| evidence | data.table | 1,075 × 105 | 2 packages |
| example_dia_skyline | data.frame | 41,820 × 16 | No other package |
| example_skyline_annotation | data.frame | 30 × 3 | No other package |
| msstats | data.frame | 1,015 × 10 | No other package |
| proteinGroups | data.table | 8 × 611 | 2 packages |
| raw.mine | data.frame | 170 × 28 | 2 packages |
| raw.om | data.frame | 860 × 13 | 2 packages |
| raw.pd | data.table | 2,858 × 50 | 2 packages |
| templateannotation | – | – | – |
| templateevidence | – | – | – |
| tmt_pd_model | list | 3 elements | No other package |
| tmt_pd_summarized | list | 2 elements | No other package |
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 package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.