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beachmat

Compiling Bioconductor to Handle Each Matrix Type


Bioconductor version: Release (3.18)

Provides a consistent C++ class interface for reading from a variety of commonly used matrix types. Ordinary matrices and several sparse/dense Matrix classes are directly supported, along with a subset of the delayed operations implemented in the DelayedArray package. All other matrix-like objects are supported by calling back into R.

Author: Aaron Lun [aut, cre], Hervé Pagès [aut], Mike Smith [aut]

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

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

Installation

To install this package, start R (version "4.3") and enter:


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

BiocManager::install("beachmat")

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")
Developer guide HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataImport, DataRepresentation, Infrastructure, Software
Version 2.18.1
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL-3
Depends
Imports methods, DelayedArray(>= 0.27.2), SparseArray, BiocGenerics, Matrix, Rcpp
System Requirements C++17
URL https://github.com/tatami-inc/beachmat
Bug Reports https://github.com/tatami-inc/beachmat/issues
See More
Suggests testthat, BiocStyle, knitr, rmarkdown, rcmdcheck, BiocParallel, HDF5Array
Linking To Rcpp
Enhances
Depends On Me
Imports Me batchelor, beachmat.hdf5, BiocSingular, DropletUtils, mumosa, scater, scran, scuttle, SingleR
Suggests Me bsseq, glmGamPoi, mbkmeans, PCAtools, scCB2
Links To Me beachmat.hdf5, BiocSingular, bsseq, dreamlet, DropletUtils, glmGamPoi, mbkmeans, PCAtools, scran, scuttle, SingleR
Build Report Build Report

Package Archives

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

Source Package beachmat_2.18.1.tar.gz
Windows Binary beachmat_2.18.1.zip (64-bit only)
macOS Binary (x86_64) beachmat_2.18.1.tgz
macOS Binary (arm64) beachmat_2.18.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/beachmat
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/beachmat
Bioc Package Browser https://code.bioconductor.org/browse/beachmat/
Package Short Url https://bioconductor.org/packages/beachmat/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive