scTypeEval
Bioc currentEvaluation of cell type classifications in single-cell transcriptomics
Release Lineage
Entered 3.23 · Apr 29, 2026
Current · Requires R 4.6
Description
scTypeEval provides tools to evaluate and validate cell type classifications in single-cell transcriptomics when ground truth labels are limited or unavailable. Results are organized in an S4 object that integrates processed data, dimensional reductions, dissimilarity assays, and consistency metrics computed across samples. The workflow includes preprocessing and feature selection, principal component analysis, computation of dissimilarity matrices, internal validation metrics (for example, silhouette-based summaries), and visualization utilities to inspect heatmaps and PCA plots. Functions support common single-cell containers and enable comparison of clustering and labeling strategies across datasets.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
81 18 exported
Complexity
3.9 avg / 16 max
Call network
81 nodes / 94 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
12,376
Files
66
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
18
Internal functions
63
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
1.16
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
75%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.6.0
System requirements
–
C++ standard
–
License
GPL-3 + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2026-04-28
Latest release
2026-04-28
Avg cadence
–
Cold removal rate
–
Dep drift
0
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 20 (1 internal)includes a package overview page
- Examples that run
- 100%19 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 99%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
Checks run against github.com/carmonalab/sctypeeval on 2026-10-21.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| black_list | list | 10 elements | No other package |
Topics
People
- Josep Garnica author maintainer
- Massimo Andreatta author
- Santiago Carmona author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("scTypeEval")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.