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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("HDF5Array")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("HDF5Array")| HDF5Array performance | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, Coverage, DataImport, DataRepresentation, GenomeAnnotation, ImmunoOncology, Infrastructure, RNASeq, Sequencing, SingleCell, Software |
| Version | 1.41.1 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.4), methods, SparseArray(>= 1.7.5), DelayedArray(>= 0.39.4), h5mread(>= 1.3.3) |
| Imports | utils, stats, tools, Matrix, BiocGenerics(>= 0.59.11), 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
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | HDF5Array_1.41.1.tar.gz |
| Windows Binary (x86_64) | HDF5Array_1.41.0.zip |
| macOS Binary (big-sur-x86_64) | HDF5Array_1.41.1.tgz |
| macOS Binary (sonoma-arm64) | HDF5Array_1.41.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/HDF5Array |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HDF5Array |
| Bioc Package Browser | https://code.bioconductor.org/browse/HDF5Array/ |
| Package Short Url | https://bioconductor.org/packages/HDF5Array/ |
| Package Downloads Report | Download Stats |