HDF5Array
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see HDF5Array.
HDF5 backend for DelayedArray objects
Bioconductor version: 3.14
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("HDF5Array")):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("HDF5Array")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | Annotation, Coverage, DataImport, DataRepresentation, GenomeAnnotation, ImmunoOncology, Infrastructure, RNASeq, Sequencing, SingleCell, Software |
| Version | 1.22.1 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8 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 |
| System Requirements | GNU make |
| URL | https://bioconductor.org/packages/HDF5Array |
| Bug Reports | https://github.com/Bioconductor/HDF5Array/issues |
See More
| Suggests | BiocParallel, GenomicRanges, SummarizedExperiment(>= 1.15.1), h5vcData, ExperimentHub, TENxBrainData, zellkonverter, GenomicFeatures, RUnit, SingleCellExperiment |
| Linking To | S4Vectors(>= 0.27.13), Rhdf5lib |
| Enhances | |
| Depends On Me | compartmap, GenoGAM, MAGAR, TENxBrainData, TENxPBMCData |
| Imports Me | biscuiteer, bsseq, Cepo, clusterExperiment, curatedTCGAData, cytomapper, DelayedTensor, DropletUtils, FRASER, GenomicScores, glmGamPoi, GSVA, HCAData, imcdatasets, LoomExperiment, MafH5.gnomAD.v3.1.1.GRCh38, methrix, MethylSeqData, minfi, MOFA2, netSmooth, NxtIRFcore, recountmethylation, scmeth, scry, signatureSearch, SingleCellMultiModal, spatialHeatmap, TabulaMurisSenisData, transformGamPoi |
| Suggests Me | beachmat, BiocSklearn, DelayedArray, DelayedMatrixStats, iSEE, MAST, mbkmeans, metabolomicsWorkbenchR, MultiAssayExperiment, PDATK, QFeatures, scMerge, scran, sesame, SummarizedExperiment, zellkonverter |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | HDF5Array_1.22.1.tar.gz |
| Windows Binary | HDF5Array_1.22.1.zip |
| macOS 10.13 (High Sierra) | HDF5Array_1.22.1.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 |
| Old Source Packages for BioC 3.14 | Source Archive |