beachmat.hdf5

This is the released version of beachmat.hdf5; for the devel version, see beachmat.hdf5.

beachmat bindings for HDF5-backed matrices

Bioconductor version: Release (3.23)

Extends beachmat to support initialization of tatami matrices from HDF5-backed arrays. This allows C++ code in downstream packages to directly call the HDF5 C/C++ library to access array data, without the need for block processing via DelayedArray. Some utilities are also provided for direct creation of an in-memory tatami matrix from a HDF5 file.

Author: Aaron Lun [aut, cre]

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>

Citation (from within R, enter citation("beachmat.hdf5")):

Seminal Bioconductor project articles:

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.

Installation

To install this package, start R (version "4.6") and enter:


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

BiocManager::install("beachmat.hdf5")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("beachmat.hdf5")

User guide	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, DataRepresentation, Infrastructure, Software
Version	1.10.0
In Bioconductor since	BioC 3.18 (R-4.3) (3 years)
License	GPL-3
Depends
Imports	methods, beachmat, HDF5Array, DelayedArray, Rcpp
System Requirements	C++17, GNU make
URL

Suggests	testthat, BiocStyle, knitr, rmarkdown, rhdf5, Matrix
Linking To	Rcpp, assorthead, beachmat, Rhdf5lib
Enhances
Depends On Me
Imports Me
Suggests Me	beachmat, sketchR
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	beachmat.hdf5_1.10.0.tar.gz
Windows Binary (x86_64)	beachmat.hdf5_1.10.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	beachmat.hdf5_1.10.0.tgz
macOS Binary (sonoma-arm64)	beachmat.hdf5_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/beachmat.hdf5
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/beachmat.hdf5
Bioc Package Browser	https://code.bioconductor.org/browse/beachmat.hdf5/
Package Short Url	https://bioconductor.org/packages/beachmat.hdf5/
Package Downloads Report	Download Stats