scater
Bioc currentSingle-Cell Analysis Toolkit for Gene Expression Data in R
Release Lineage
Entered 3.3 · May 4, 2016
Current · Requires R 4.6
Description
A collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control and visualization.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
81 41 exported
Complexity
5.3 avg / 38 max
Call network
81 nodes / 91 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
11,436
Files
100
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
86
Internal functions
40
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.36
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
21
First release
2016-06-12
Latest release
2026-06-30
Avg cadence
186 days
Cold removal rate
100%
Dep drift
48
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 39 (1 internal)
- Examples that run
- 94%33 run in a plain check · 2 never run
- Exported functions with examples
- 97%
- Documented parameters
- 94%
- Return-value docs
- 97%
- Help pages citing references
- 10%
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
2 practices detected in the Bioconductor git repository
Topics
Depended on by (54)
Show 62 packagesHide 62 packages
Bioconductor (52)
CRAN (2)
Suggested by (128)
People
- Alan O'Callaghan contributor maintainer
- Tuomas Borman contributor
- Kieran Campbell author
- Felix G.M. Ernst contributor
- Vladimir Kiselev contributor
- Leo Lahti contributor
- Aaron Lun author contributor
- Davis McCarthy author
- Yun Peng contributor
- Quin Wills author
Cite
Cite this package
Run in R for the authors' entry:
citation("scater")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioinformatics/btw777.
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.