tidySummarizedExperiment
Bioc currentBrings SummarizedExperiment to the Tidyverse
Release Lineage
Entered 3.12 · Oct 28, 2020
Current · Requires R 4.6
Description
The tidySummarizedExperiment package provides a set of tools for creating and manipulating tidy data representations of SummarizedExperiment objects. SummarizedExperiment is a widely used data structure in bioinformatics for storing high-throughput genomic data, such as gene expression or DNA sequencing data. The tidySummarizedExperiment package introduces a tidy framework for working with SummarizedExperiment objects. It allows users to convert their data into a tidy format, where each observation is a row and each variable is a column. This tidy representation simplifies data manipulation, integration with other tidyverse packages, and enables seamless integration with the broader ecosystem of tidy tools for data analysis.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
114 2 exported
Complexity
3.6 avg / 26 max
Call network
114 nodes / 228 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
10,480
Files
85
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
3
Internal functions
112
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.35
testthat edition
–
Docs
Roxygen coverage
66.7%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
8.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.3.0
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
8
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 34 (2 internal)includes a package overview page
- Examples that run
- 97%30 run in a plain check · 1 hold no code
- Exported functions with examples
- 100%
- Documented parameters
- 90%
- Return-value docs
- 100%
- Help pages citing references
- 91%
Repository practices
10 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/stemangiola/tidysummarizedexperiment on 2026-10-22.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
Datasets
Topics
Depended on by (1)
Bioconductor (1)
Suggested by (3)
People
- Stefano Mangiola author maintainer
Cite
Cite this package
Run in R for the authors' entry:
citation("tidySummarizedExperiment")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 v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.