HDF5Array

This is thereleased version of HDF5Array; for the devel version, seeHDF5Array.

HDF5 datasets as array-like objects in R

DOI: 10.18129/B9.bioc.HDF5Array

Bioconductor version: Release (3.22)

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] ORCID: 0009-0002-8272-4522

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

Citation (from within R, entercitation("HDF5Array")):

Installation

To install this package, start R (version "4.5") and enter:

if (!require("BiocManager", quietly = TRUE))    install.packages("BiocManager")BiocManager::install("HDF5Array")

For older versions of R, please refer to the appropriateBioconductor 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	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation,Coverage,DataImport,DataRepresentation,GenomeAnnotation,ImmunoOncology,Infrastructure,RNASeq,Sequencing,SingleCell,Software
Version	1.38.0
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

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	MAGAR,TENxBrainData,TENxPBMCData
Imports Me	alabaster.matrix,beachmat.hdf5,BgeeDB,biscuiteer,bsseq,Cepo,chihaya,clusterExperiment,CuratedAtlasQueryR,cytomapper,DelayedTensor,DropletUtils,FRASER,GenomicScores,glmGamPoi,GSVA,lemur,LoomExperiment,mariner,methodical,methrix,minfi,MOFA2,netSmooth,orthos,recountmethylation,scmeth,signatureSearch,SpliceWiz,TENxIO,transformGamPoi,vmrseq,xenLite,MafH5.gnomAD.v4.0.GRCh38,curatedTCGAData,HCAData,HCATonsilData,imcdatasets,MerfishData,MethylSeqData,orthosData,scMultiome,SingleCellMultiModal,TabulaMurisSenisData,TumourMethData,ebvcube,rliger
Suggests Me	beachmat,BiocGenerics,BiocSklearn,cellxgenedp,DeconvoBuddies,DelayedArray,DelayedMatrixStats,h5mread,iSEE,MAST,mbkmeans,MuData,MultiAssayExperiment,PDATK,QFeatures,S4Arrays,SCArray,scMerge,scran,scry,SparseArray,SummarizedExperiment,zellkonverter,STexampleData,spicyWorkflow,BigDataStatMeth,SeuratObject
Links To Me
Build Report	Build Report

Package Archives

FollowInstallation instructions to use this package in your R session.

Source Package	HDF5Array_1.38.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)	HDF5Array_1.37.0.tgz
macOS Binary (arm64)	HDF5Array_1.38.0.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

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