MSstatsBioNet
Bioc currentNetwork Analysis for MS-based Proteomics Experiments
Release Lineage
Entered 3.21 · Apr 16, 2025
Current · Requires R 4.6
Description
A set of tools for network analysis using mass spectrometry-based proteomics data and network databases. The package takes as input the output of MSstats differential abundance analysis and provides functions to perform enrichment analysis and visualization in the context of prior knowledge from past literature. Notably, this package integrates with INDRA, which is a database of biological networks extracted from the literature using text mining techniques.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
49 9 exported
Complexity
5.7 avg / 30 max
Call network
49 nodes / 44 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
4,675
Files
50
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
9
Internal functions
40
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.54
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.4.0
System requirements
–
C++ standard
–
License
file LICENSE
License flags
SPDX valid, not OSI
History
Versions
3
First release
2025-04-15
Latest release
2026-04-30
Avg cadence
190 days
Cold removal rate
100%
Dep drift
8
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 16
- Examples that run
- 43%3 run in a plain check · 4 never run
- Exported functions with examples
- 78%
- Documented parameters
- 97%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
7 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/vitek-lab/msstatsbionet on 2026-10-21.
GitHub Pages site last deployed 2026-10-14 · The repository has a site deploy workflow
pkgdown site last built 2026-10-14
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| garrido-2024 | data.frame | 22 × 8 | No other package |
| groupComparisonModel | data.frame | 10 × 17 | No other package |
| indraResponse | list | 25 elements | No other package |
| msstats | data.frame | 2,668 × 12 | No other package |
| subnetwork | list | 2 elements | No other package |
Topics
Depended on by (1)
Bioconductor (1)
People
- Anthony Wu author maintainer
- Olga Vitek author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("MSstatsBioNet")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 v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.