scDiagnostics
Bioc currentCell type annotation diagnostics
Release Lineage
Entered 3.20 · Oct 30, 2024
Current · Requires R 4.6
Description
The scDiagnostics package provides diagnostic plots to assess the quality of cell type assignments from single cell gene expression profiles. The implemented functionality allows to assess the reliability of cell type annotations, investigate gene expression patterns, and explore relationships between different cell types in query and reference datasets allowing users to detect potential misalignments between reference and query datasets. The package also provides visualization capabilities for diagnostics purposes.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
69 32 exported
Complexity
14.9 avg / 90 max
Call network
69 nodes / 146 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
25,907
Files
169
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
32
Internal functions
37
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.29
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.4.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
4
First release
2024-10-29
Latest release
2026-07-07
Avg cadence
197 days
Cold removal rate
100%
Dep drift
10
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 60 (34 internal)includes a package overview page
- Examples that run
- 100%33 run in a plain check
- Exported functions with examples
- 94%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 22%
Repository practices
8 development-tooling and community-health practices detected across 5 families in the upstream repository
Checks run against github.com/ccb-hms/scdiagnostics on 2026-10-22.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2026-09-23 · The repository has a site deploy workflow
Show all practicesHide 1 practice
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| qc_data | – | – | – |
| query_data | – | – | – |
| reference_data | – | – | – |
Topics
People
- Anthony Christidis author maintainer
- Smriti Chawla author
- Ludwig Geistlinger author
- Robert Gentleman author
- Andrew Ghazi author
- Nitesh Turaga contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("scDiagnostics")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
The repository also keeps a CITATION.cff.
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.