artMS
Bioc currentAnalytical R tools for Mass Spectrometry
Release Lineage
Entered 3.8 · Oct 31, 2018
Current · Requires R 4.6
Description
artMS provides a set of tools for the analysis of proteomics label-free datasets. It takes as input the MaxQuant search result output (evidence.txt file) and performs quality control, relative quantification using MSstats, downstream analysis and integration. artMS also provides a set of functions to re-format and make it compatible with other analytical tools, including, SAINTq, SAINTexpress, Phosfate, and PHOTON. Check [http://artms.org](http://artms.org) for details.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
82 33 exported
Complexity
12.5 avg / 210 max
Call network
82 nodes / 124 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
18,225
Files
169
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
33
Internal functions
49
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
40%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1.0
System requirements
–
C++ standard
–
License
GPL (>= 3) + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
16
First release
2019-04-07
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
9
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 44
- Examples that run
- 79%26 run in a plain check · 7 never run
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- Learn to use artMS HTML
Repository practices
3 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/biodavidjm/artms on 2026-10-11.
GitHub Pages site last deployed 2023-06-29
pkgdown site last built 2021-07-14
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| artms_config | list | 5 elements | No other package |
| artms_data_corum_mito_database | data.frame | 3,616 × 20 | No other package |
| artms_data_pathogen_LPN | data.frame | 2,930 × 1 | No other package |
| artms_data_pathogen_TB | data.frame | 4,222 × 1 | No other package |
| artms_data_ph_config | list | 5 elements | No other package |
| artms_data_ph_contrast | vector | 1 element | No other package |
| artms_data_ph_evidence | data.frame | 5,004 × 36 | No other package |
| artms_data_ph_keys | data.frame | 4 × 5 | No other package |
| artms_data_ph_msstats_modelqc | data.frame | 24,162 × 13 | No other package |
| artms_data_ph_msstats_results | data.frame | 3,413 × 11 | No other package |
| artms_data_randomDF | data.frame | 100 × 10 | No other package |
Topics
People
- David Jimenez-Morales author maintainer
- Nevan Krogan author
- Alexandre Rosa Campos author contributor
- Danielle Swaney author contributor
- John Von Dollen author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("artMS")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 v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.