simpleSingleCell
Bioc currentA step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor
Release Lineage
Entered 3.4 · Oct 18, 2016
Current · Requires R 4.6
Description
Once a proud workflow package, this is now a shell of its former self. Almost all of its content has been cannibalized for use in the "Orchestrating Single-Cell Analyses with Bioconductor" book at https://osca.bioconductor.org. Most vignettes here are retained as reminders of the glory that once was, also providing redirection for existing external links to the relevant OSCA book chapters.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
8 6 exported
Complexity
2.9 avg / 6 max
Call network
8 nodes / 4 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
2,235
Files
30
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
6
Internal functions
2
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
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
–
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
20
First release
2016-10-17
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
57
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 6
- Examples that run
- 100%5 run in a plain check
- Exported functions with examples
- 83%
- Documented parameters
- 95%
- Return-value docs
- 83%
- Help pages citing references
- 0%
- 05. Correcting batch effects HTML
- 12. Scalability for big data HTML
- 10. Detecting differential expression HTML
- 08. Detecting doublets HTML
- 01. Introduction HTML
- 13. Further analysis strategies HTML
- 11. Advanced batch correction HTML
- 06. Quality control details HTML
- 02. Read count data HTML
- 07. Spike-in normalization HTML
Show 3 moreHide 3 vignettes
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Topics
People
- Aaron Lun author maintainer
- John Marioni author
- Davis McCarthy author
Cite
Cite this package
Run in R for the authors' entry:
citation("simpleSingleCell")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.12688/f1000research.9501.2.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.