scp
Bioc currentMass Spectrometry-Based Single-Cell Proteomics Data Analysis
Release Lineage
Entered 3.12 · Oct 28, 2020
Current · Requires R 4.6
Description
Utility functions for manipulating, processing, and analyzing mass spectrometry-based single-cell proteomics data. The package is an extension to the 'QFeatures' package and relies on 'SingleCellExpirement' to enable single-cell proteomics analyses. The package offers the user the functionality to process quantitative table (as generated by MaxQuant, Proteome Discoverer, and more) into data tables ready for downstream analysis and data visualization.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
148 36 exported
Complexity
2.4 avg / 12 max
Call network
148 nodes / 175 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
17,236
Files
92
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
38
Internal functions
101
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
1.27
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
6.3%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.3.0
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
182 days
Cold removal rate
100%
Dep drift
11
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 24
- Examples that run
- 100%20 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 99%
- Return-value docs
- 61%
- Help pages citing references
- 33%
Repository practices
6 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/uclouvain-cbio/scp on 2026-10-21.
The R CMD check workflow runs on Linux and macOS, and on R-devel
GitHub Pages site last deployed 2025-05-31 · The repository has a site deploy workflow
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| leduc_minimal | – | – | – |
| mqScpData | data.frame | 1,361 × 149 | No other package |
| sampleAnnotation | data.frame | 64 × 6 | No other package |
| scp1 | – | – | – |
Topics
Suggested by (1)
People
- Christophe Vanderaa author maintainer
- Laurent Gatto author
- Léopold Guyot contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("scp")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/s13059-025-03713-4.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.