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.
None published for Bioconductor
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
7,566
Files
65
Compiled share
6%
Has compiled src
Yes
Language breakdown
API
Exported functions
25
Internal functions
41
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.55
testthat edition
–
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 externalC++17
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
14
First release
2020-04-08
Latest release
2026-09-10
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
- Help pages
- 16
- Examples that run
- 100%15 run in a plain check
- Exported functions with examples
- 94%
- Documented parameters
- 88%
- Return-value docs
- 100%
- Help pages citing references
- 13%
- Bugfix to
SingleR()to respect non-defaultassay.type.ref=.
From inst/NEWS.Rd in the release
Repository practices
2 development-tooling and community-health practices detected across 1 family in the upstream repository
Checks run against github.com/singler-inc/singler on 2026-10-18.
The R CMD check workflow runs on Linux, and on R-devel
Topics
Depended on by (9)
Show all 16 packagesHide all 16 packages
Bioconductor (9)
Suggested by (7)
People
- Aaron Lun contributor maintainer
- Jared Andrews contributor
- Dvir Aran author copyright holder
- Daniel Bunis contributor
- Friederike Dündar contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("SingleR")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1038/s41590-018-0276-y.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.