HDF5Array
This is the development version of HDF5Array; for the stable release version, see HDF5Array.
HDF5 datasets as array-like objects in R
Bioconductor version: Development (3.23)
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.
Author: Hervé Pagès [aut, cre]
Maintainer: Hervé Pagès <hpages.on.github at gmail.com>
citation("HDF5Array")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("HDF5Array")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | Annotation, Coverage, DataImport, DataRepresentation, GenomeAnnotation, ImmunoOncology, Infrastructure, RNASeq, Sequencing, SingleCell, Software |
| Version | 1.39.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (9.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.4), methods, SparseArray(>= 1.7.5), DelayedArray(>= 0.33.5), h5mread(>= 0.99.4) |
| Imports | utils, stats, tools, Matrix, BiocGenerics(>= 0.51.2), S4Vectors, IRanges, S4Arrays(>= 1.1.1), rhdf5 |
| System Requirements | |
| URL | https://bioconductor.org/packages/HDF5Array |
| Bug Reports | https://github.com/Bioconductor/HDF5Array/issues |
See More
| Suggests | BiocParallel, GenomicRanges, SummarizedExperiment(>= 1.15.1), h5vcData, ExperimentHub, TENxBrainData, zellkonverter, GenomicFeatures, SingleCellExperiment, DelayedMatrixStats, genefilter, RSpectra, RUnit, knitr, rmarkdown, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/HDF5Array |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HDF5Array |
| Package Short Url | https://bioconductor.org/packages/HDF5Array/ |
| Package Downloads Report | Download Stats |