scGPS
Bioc currentA complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)
Release Lineage
Entered 3.10 · Oct 30, 2019
Current · Requires R 4.6
Description
The package implements two main algorithms to answer two key questions: a SCORE (Stable Clustering at Optimal REsolution) to find subpopulations, followed by scGPS to investigate the relationships between subpopulations.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
61 38 exported
Complexity
4.5 avg / 36 max
Call network
61 nodes / 45 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
5,813
Files
70
Compiled share
8.2%
Has compiled src
Yes
Language breakdown
API
Exported functions
38
Internal functions
0
Testing
Has tests
Yes
Test-to-code ratio
0.01
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
100%
Unsafe pattern score
0
Dep constraint coverage
11.8%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.6
System requirements
1 externalGNU make
C++ standard
–
License
GPL-3
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
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 42
- Examples that run
- 100%38 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 94%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
1 development-tooling and community-health practice detected across 1 family in the upstream repository
Checks run against github.com/imb-computational-genomics-lab/scgps on 2026-10-21.
GitHub Pages site last deployed 2020-12-16
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| day_2_cardio_cell_sample | list | 3 elements | No other package |
| day_5_cardio_cell_sample | list | 3 elements | No other package |
| training_gene_sample | data.frame | 158 × 1 | No other package |
Topics
People
- Quan Nguyen author maintainer
- Anne Senabouth author
- Michael Thompson author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("scGPS")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 v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.