tidySingleCellExperiment
Bioc currentBrings SingleCellExperiment to the Tidyverse
Release Lineage
Entered 3.12 · Oct 28, 2020
Current · Requires R 4.6
Description
'tidySingleCellExperiment' is an adapter that abstracts the 'SingleCellExperiment' container in the form of a 'tibble'. This allows *tidy* data manipulation, nesting, and plotting. For example, a 'tidySingleCellExperiment' is directly compatible with functions from 'tidyverse' packages `dplyr` and `tidyr`, as well as plotting with `ggplot2` and `plotly`. In addition, the package provides various utility functions specific to single-cell omics data analysis (e.g., aggregation of cell-level data to pseudobulks).
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
86 3 exported
Complexity
2 avg / 9 max
Call network
86 nodes / 103 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
8,212
Files
86
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
4
Internal functions
81
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.19
testthat edition
–
Docs
Roxygen coverage
75%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
4.2%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.4.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
12
First release
2020-10-27
Latest release
2026-04-28
Avg cadence
186 days
Cold removal rate
100%
Dep drift
11
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 45 (5 internal)includes a package overview page
- Examples that run
- 95%35 run in a plain check · 2 hold no code
- Exported functions with examples
- 100%
- Documented parameters
- 93%
- Return-value docs
- 100%
- Help pages citing references
- 82%
Repository practices
10 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/stemangiola/tidysinglecellexperiment on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| cell_type_df | tibble | 80 × 2 | 2 packages |
| pbmc_small | – | – | – |
| pbmc_small_nested_interactions | tibble | 100 × 9 | 2 packages |
Topics
Depended on by (2)
Bioconductor (2)
Suggested by (4)
People
- Stefano Mangiola author maintainer
Cite
Cite this package
Run in R for the authors' entry:
citation("tidySingleCellExperiment")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1038/s41592-024-02299-2.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.