MSstatsLiP
Bioc currentLiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments
Release Lineage
Entered 3.14 · Oct 27, 2021
Current · Requires R 4.6
Description
Tools for LiP peptide and protein significance analysis. Provides functions for summarization, estimation of LiP peptide abundance, and detection of changes across conditions. Utilizes functionality across the MSstats family of packages.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
42 18 exported
Complexity
5.1 avg / 26 max
Call network
42 nodes / 33 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
8,353
Files
77
Compiled share
2.1%
Has compiled src
Yes
Language breakdown
API
Exported functions
18
Internal functions
21
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
–
Unsafe pattern score
0
Dep constraint coverage
4.5%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
10
First release
2021-10-26
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 27 (1 internal)includes a package overview page
- Examples that run
- 100%26 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
3 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/vitek-lab/msstatslip on 2026-10-21.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| LiPRawData | data.table | 422 × 29 | No other package |
| MSstatsLiP_Summarized | list | 2 elements | No other package |
| MSstatsLiP_data | list | 2 elements | No other package |
| MSstatsLiP_model | list | 3 elements | No other package |
| SkylineTest | data.table | 2,115 × 13 | No other package |
| TrPRawData | data.table | 911 × 29 | No other package |
| raw_lip | spec_tbl_df | 6,944 × 29 | No other package |
| raw_prot | spec_tbl_df | 9,120 × 29 | No other package |
Topics
People
- Anthony Wu author maintainer
- Valentina Cappelletti author
- Meena Choi author
- Ting Huang author
- Devon Kohler author
- Liliana Malinovska author
- Deril Raju author
- Mateusz Staniak author
- Tsung-Heng Tsai author
- Olga Vitek author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("MSstatsLiP")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.