HDF5Array
Bioc currentHDF5 datasets as array-like objects in R
Release Lineage
Entered 3.3 · May 4, 2016
Current · Requires R 4.6
Description
The HDF5Array package is an HDF5 backend for DelayedArray objects. It implements the HDF5Array, H5SparseMatrix, H5ADMatrix, and TENxMatrix classes, 4 convenient and memory-efficient array-like containers for representing and manipulating either: (1) a conventional (a.k.a. dense) HDF5 dataset, (2) an HDF5 sparse matrix (stored in CSR/CSC/Yale format), (3) the central matrix of an h5ad file (or any matrix in the /layers group), or (4) a 10x Genomics sparse matrix. All these containers are DelayedArray extensions and thus support all operations (delayed or block-processed) supported by DelayedArray objects.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
140 45 exported
Complexity
3 avg / 14 max
Call network
140 nodes / 191 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
6,482
Files
73
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
47
Internal functions
93
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
38.5%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.4
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
21
First release
2016-05-27
Latest release
2026-04-28
Avg cadence
178 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
- Examples that run
- 100%
- Documented parameters
- 59%
- Return-value docs
- 93%
- References docs
- 27%
Topics
Depended on by (91)
Bioconductor (87)
CRAN (4)
People
- Hervé Pagès author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("HDF5Array")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.