MSstatsPTM
Bioc currentStatistical Characterization of Post-translational Modifications
Release Lineage
Entered 3.12 · Oct 28, 2020
Current · Requires R 4.6
Description
MSstatsPTM provides general statistical methods for quantitative characterization of post-translational modifications (PTMs). Supports DDA, DIA, SRM, and tandem mass tag (TMT) labeling. Typically, the analysis involves the quantification of PTM sites (i.e., modified residues) and their corresponding proteins, as well as the integration of the quantification results. MSstatsPTM provides functions for summarization, estimation of PTM site abundance, and detection of changes in PTMs across experimental conditions.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
95 22 exported
Complexity
6 avg / 32 max
Call network
95 nodes / 89 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
11,736
Files
124
Compiled share
0.6%
Has compiled src
Yes
Language breakdown
API
Exported functions
22
Internal functions
70
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
5.6%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.3
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
12
First release
2020-10-27
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
100%
Dep drift
20
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 46 (6 internal)includes a package overview page
- Examples that run
- 97%37 run in a plain check · 1 hold no code
- Exported functions with examples
- 95%
- Documented parameters
- 80%
- Return-value docs
- 95%
- Help pages citing references
- 0%
Repository practices
7 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/vitek-lab/msstatsptm on 2026-10-18.
GitHub Pages site last deployed 2026-10-15 · The repository has a site deploy workflow
pkgdown site last built 2026-10-15
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| fragpipe_annotation | data.frame | 60 × 7 | No other package |
| fragpipe_annotation_protein | data.frame | 90 × 7 | No other package |
| fragpipe_input | data.frame | 346 × 29 | No other package |
| fragpipe_input_protein | data.frame | 47 × 27 | No other package |
| maxq_lf_annotation | data.frame | 33 × 5 | No other package |
| maxq_lf_evidence | data.frame | 492 × 63 | No other package |
| maxq_tmt_annotation | data.frame | 30 × 7 | No other package |
| maxq_tmt_evidence | data.frame | 199 × 96 | No other package |
| pd_annotation | data.frame | 36 × 3 | No other package |
| pd_psm_input | data.frame | 1,657 × 60 | No other package |
| pd_testing_output | list | 2 elements | No other package |
| raw.input | list | 2 elements | No other package |
| raw.input.tmt | list | 2 elements | No other package |
| spectronaut_annotation | data.frame | 36 × 5 | No other package |
| spectronaut_input | data.frame | 2,683 × 23 | No other package |
| summary.data | list | 2 elements | No other package |
| summary.data.tmt | list | 2 elements | No other package |
Topics
Depended on by (2)
Bioconductor (2)
People
- Anthony Wu author maintainer
- Meena Choi author
- Ting Huang author
- Devon Kohler author
- Deril Raju author
- Mateusz Staniak author
- Tsung-Heng Tsai author
- Olga Vitek author
Cite
Cite this package
Run in R for the authors' entry:
citation("MSstatsPTM")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 v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.