SingleR
Bioc currentReference-Based Single-Cell RNA-Seq Annotation
Release Lineage
Entered 3.10 · Oct 30, 2019
Current · Requires R 4.6
Description
Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer the cell of origin of each single cell independently.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
81 25 exported
Complexity
3.9 avg / 16 max
Call network
81 nodes / 86 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
7,554
Files
69
Compiled share
6%
Has compiled src
Yes
Language breakdown
API
Exported functions
25
Internal functions
41
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.54
testthat edition
–
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
10%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
1
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
14
First release
2020-04-08
Latest release
2026-07-07
Avg cadence
182 days
Cold removal rate
100%
Dep drift
14
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
- 88%
- Return-value docs
- 100%
- References docs
- 13%
Topics
Depended on by (15)
People
- Aaron Lun contributor maintainer
- Jared Andrews contributor
- Dvir Aran author cph
- Daniel Bunis contributor
- Friederike Dündar contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("SingleR")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 v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.