HDF5Array

DOI: 10.18129/B9.bioc.HDF5Array    

HDF5 backend for DelayedArray objects

Bioconductor version: Release (3.13)

Implement 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

Maintainer: Hervé Pagès <hpages.on.github at gmail.com>

Citation (from within R, enter citation("HDF5Array")):

Installation

To install this package, start R (version "4.1") 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.

Documentation

PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, Coverage, DataImport, DataRepresentation, GenomeAnnotation, ImmunoOncology, Infrastructure, RNASeq, Sequencing, SingleCell, Software
Version 1.20.0
In Bioconductor since BioC 3.3 (R-3.3) (5 years)
License Artistic-2.0
Depends R (>= 3.4), methods, DelayedArray(>= 0.15.16), rhdf5(>= 2.31.6)
Imports utils, stats, tools, Matrix, rhdf5filters, BiocGenerics(>= 0.31.5), S4Vectors, IRanges
LinkingTo S4Vectors(>= 0.27.13), Rhdf5lib
Suggests BiocParallel, GenomicRanges, SummarizedExperiment(>= 1.15.1), h5vcData, ExperimentHub, TENxBrainData, zellkonverter, GenomicFeatures, RUnit, SingleCellExperiment
SystemRequirements GNU make
Enhances
URL https://bioconductor.org/packages/HDF5Array
BugReports https://github.com/Bioconductor/HDF5Array/issues
Depends On Me compartmap, GenoGAM, MAGAR, TENxBrainData, TENxPBMCData
Imports Me biscuiteer, bsseq, clusterExperiment, curatedTCGAData, cytomapper, DropletUtils, FRASER, GenomicScores, glmGamPoi, GSVA, HCAData, imcdatasets, LoomExperiment, MafH5.gnomAD.r3.0.GRCh38, MafH5.gnomAD.v3.1.1.GRCh38, methrix, MethylSeqData, minfi, MOFA2, netSmooth, recountmethylation, scmeth, scry, signatureSearch, SingleCellMultiModal, spatialHeatmap
Suggests Me beachmat, BiocSklearn, DelayedArray, DelayedMatrixStats, iSEE, MAST, mbkmeans, metabolomicsWorkbenchR, MultiAssayExperiment, PDATK, QFeatures, scMerge, scran, sesame, SummarizedExperiment, zellkonverter
Links To Me
Build Report  

Package Archives

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

Source Package HDF5Array_1.20.0.tar.gz
Windows Binary HDF5Array_1.20.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) HDF5Array_1.20.0.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 https://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: