HDF5Array

DOI: 10.18129/B9.bioc.HDF5Array    

This is the development version of HDF5Array; for the stable release version, see HDF5Array.

HDF5 backend for DelayedArray objects

Bioconductor version: Development (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")):

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("HDF5Array", version = "devel")

Documentation

PDF   Reference Manual

Details

biocViews Annotation, Coverage, DataImport, DataRepresentation, GenomeAnnotation, Infrastructure, RNASeq, Sequencing, SingleCell, Software
Version 1.9.19
In Bioconductor since BioC 3.3 (R-3.3) (2.5 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 TENxBrainData, TENxPBMCData
Imports Me beachmat, bsseq, clusterExperiment, DelayedMatrixStats, DropletUtils, minfi, scmeth
Suggests Me BiocSklearn, DelayedArray, MultiAssayExperiment, scran, SummarizedExperiment
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package HDF5Array_1.9.19.tar.gz
Windows Binary HDF5Array_1.9.19.zip
Mac OS X 10.11 (El Capitan) HDF5Array_1.9.19.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: