scPCA
Bioc currentSparse Contrastive Principal Component Analysis
Release Lineage
Entered 3.10 · Oct 30, 2019
Current · Requires R 4.6
Description
A toolbox for sparse contrastive principal component analysis (scPCA) of high-dimensional biological data. scPCA combines the stability and interpretability of sparse PCA with contrastive PCA's ability to disentangle biological signal from unwanted variation through the use of control data. Also implements and extends cPCA.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
13 1 exported
Complexity
7.6 avg / 16 max
Call network
13 nodes / 23 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
5,834
Files
74
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
1
Internal functions
12
Testing & CI
Has tests
Yes
Test-to-code ratio
1.01
testthat edition
–
CI present
Yes
CI type
["travis","appveyor"]
PR gated
No
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
4.0.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
14
First release
2019-10-29
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
8
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- 83%
- Return-value docs
- 100%
- References docs
- 60%
Topics
Depended on by (2)
Bioconductor (2)
People
- Philippe Boileau author maintainer cph
- Sandrine Dudoit contributor ths
- Nima Hejazi author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("scPCA")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.