This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see HDF5Array.
Bioconductor version: 3.8
Implements the HDF5Array and TENxMatrix classes, 2 convenient and memory-efficient array-like containers for on-disk representation of HDF5 datasets. HDF5Array is for datasets that use the conventional (i.e. dense) HDF5 representation. TENxMatrix is for datasets that use the HDF5-based sparse matrix representation from 10x Genomics (e.g. the 1.3 Million Brain Cell Dataset). Both containers being DelayedArray extensions, they support all operations supported by DelayedArray objects. These operations can be either delayed or block-processed.
Author: Hervé Pagès
Maintainer: Hervé Pagès <hpages at fredhutch.org>
Citation (from within R,
enter citation("HDF5Array")
):
To install this package, start R (version "3.5") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("HDF5Array")
For older versions of R, please refer to the appropriate Bioconductor release.
Reference Manual | ||
Text | NEWS |
biocViews | Annotation, Coverage, DataImport, DataRepresentation, GenomeAnnotation, ImmunoOncology, Infrastructure, RNASeq, Sequencing, SingleCell, Software |
Version | 1.10.1 |
In Bioconductor since | BioC 3.3 (R-3.3) (3 years) |
License | Artistic-2.0 |
Depends | R (>= 3.4), methods, DelayedArray(>= 0.7.41), rhdf5(>= 2.25.6) |
Imports | utils, tools, BiocGenerics(>= 0.25.1), S4Vectors, IRanges |
LinkingTo | |
Suggests | h5vcData, SummarizedExperiment(>= 1.9.6), GenomicRanges, ExperimentHub, BiocParallel, BiocStyle |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | GenoGAM, TENxBrainData, TENxPBMCData |
Imports Me | beachmat, bsseq, clusterExperiment, DelayedMatrixStats, DropletUtils, LoomExperiment, minfi, scmeth |
Suggests Me | BiocSklearn, DelayedArray, MultiAssayExperiment, scran, SummarizedExperiment |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | HDF5Array_1.10.1.tar.gz |
Windows Binary | HDF5Array_1.10.1.zip |
Mac OS X 10.11 (El Capitan) | HDF5Array_1.10.1.tgz |
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 | http://bioconductor.org/packages/HDF5Array/ |
Package Downloads Report | Download Stats |
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