BumpyMatrix
Bioc currentBumpy Matrix of Non-Scalar Objects
Release Lineage
Entered 3.13 · May 20, 2021
Current · Requires R 4.6
Description
Implements the BumpyMatrix class and several subclasses for holding non-scalar objects in each entry of the matrix. This is akin to a ragged array but the raggedness is in the third dimension, much like a bumpy surface - hence the name. Of particular interest is the BumpyDataFrameMatrix, where each entry is a Bioconductor data frame. This allows us to naturally represent multivariate data in a format that is compatible with two-dimensional containers like the SummarizedExperiment and MultiAssayExperiment objects.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
16 3 exported
Complexity
3 avg / 8 max
Call network
16 nodes / 16 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
2,711
Files
25
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
5
Internal functions
13
Testing
Has tests
Yes
Test-to-code ratio
0.58
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
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
11
First release
2021-07-03
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 5
- Examples that run
- 100%5 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 67%
- Return-value docs
- 67%
- Help pages citing references
- 0%
Repository practices
1 development-tooling and community-health practice detected across 1 family in the upstream repository
Checks run against github.com/ltla/bumpymatrix on 2026-10-11.
The repository owner accepts GitHub Sponsors
Topics
Depended on by (10)
Show all 16 packagesHide all 16 packages
Bioconductor (10)
Suggested by (6)
People
- Aaron Lun author maintainer
- Genentech, Inc. copyright holder
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("BumpyMatrix")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
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.