SingleCellExperiment
Bioc currentS4 Classes for Single Cell Data
Release Lineage
Entered 3.6 · Oct 31, 2017
Current · Requires R 4.6
Description
Defines a S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
52 9 exported
Complexity
3.3 avg / 17 max
Call network
52 nodes / 17 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
9,244
Files
82
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
61
Internal functions
41
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.60
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
18
First release
2017-10-30
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
83.3%
Dep drift
3
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 25
- Examples that run
- 100%23 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 95%
- Return-value docs
- 56%
- Help pages citing references
- 0%
counts(),logcounts()and other named getters/setters will now raise a warning ifi=is specified, rather than silently treating it as the next argument toassay()(usuallywithDimnames=).
From inst/NEWS.Rd in the release
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
1 practice detected in the Bioconductor git repository
Topics
Depended on by (302)
Show 68 packagesHide 68 packages
Bioconductor (294)
Suggested by (89)
People
- Davide Risso author maintainer copyright holder
- Keegan Korthauer contributor
- Aaron Lun author copyright holder
- Kevin Rue-Albrecht contributor
-
Luke Zappia
contributor
lazappi
Cite
Cite this package
Run in R for the authors' entry:
citation("SingleCellExperiment")The package provides a citation file, so citation() returns the authors' own entry.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.