Skip to content

MSstatsTMT

Bioc current

Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

v2.20.0 · software · Artistic-2.0
View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.8 · Oct 31, 2018

Current · Requires R 4.6

1.0 In 16 of 49 releases 3.23

Description

The package provides statistical tools for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling. It provides multiple functionalities, including aata visualization, protein quantification and normalization, and statistical modeling and inference. Furthermore, it is inter-operable with other data processing tools, such as Proteome Discoverer, MaxQuant, OpenMS and SpectroMine.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

77 9 exported

Complexity

3.1 avg / 26 max

Call network

77 nodes / 72 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

Open call graph →
Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

Code

Structure

Lines of code

5,848

Files

98

Compiled share

0%

Has compiled src

No

Language breakdown

R 3,208 (54.9%)Tests 120 (2.1%)Docs 2,131 (36.4%)Vignettes 389 (6.7%)

API

Exported functions

9

Internal functions

68

Recent export changes

v3.8+6 MaxQtoMSstatsTMTFormat, PDtoMSstatsTMTFormat, SpectroMinetoMSstatsTMTFormat +3 more

Testing & CI

Has tests

Yes

Test-to-code ratio

0.04

testthat edition

–

CI present

Yes

CI type

["travis"]

PR gated

No

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

0%

Unsafe pattern score

0

Dep constraint coverage

0%

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

16

First release

2019-02-25

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

–

Dep drift

13

LOC over versions

v3.8: 4,060 LOCv3.9: 4,601 LOCv3.10: 5,517 LOCv3.11: 5,599 LOCv3.12: 5,615 LOCv3.13: 4,934 LOCv3.14: 5,166 LOCv3.15: 5,166 LOCv3.16: 5,171 LOCv3.17: 5,171 LOCv3.18: 5,171 LOCv3.19: 5,848 LOCv3.20: 5,848 LOCv3.21: 5,848 LOCv3.22: 5,848 LOCv3.23: 5,848 LOC

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

Documentation
READMEYes · 41 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo
Examples that run
100%
Documented parameters
100%
Return-value docs
100%
References docs
0%

Topics

Software › ResearchField › Immunology › ImmunoOncology
Software › Technology › MassSpectrometry
Software › ResearchField › Proteomics
Software

Depended on by (4)

Bioconductor (4)

MSstatsPTM MSstatsResponse MSstatsShiny MSstatsTMTPTM

People

Report a problem with this page →