Package: beachmat 2.29.0

Aaron Lun

beachmat: Compiling Bioconductor to Handle Each Matrix Type

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.

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

beachmat_2.29.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
beachmat/json (API)
NEWS

# Install 'beachmat' in R:
install.packages('beachmat', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/tatami-inc/beachmat/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:beachmat-2.29.0(bioc 3.24)beachmat-2.28.0(bioc 3.23)

datarepresentationdataimportinfrastructurebioconductor-packagehuman-cell-atlasmatrix-librarycpp

11.24 score 5 stars 191 packages 26 scripts 31k downloads 3 mentions 39 exports 15 dependencies

Last updated from:de69b77e7c. Checks:12 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING237
linux-devel-arm64WARNING418
linux-devel-x86_64WARNING531
source / vignettesOK318
linux-release-arm64WARNING381
linux-release-x86_64WARNING513
macos-release-arm64WARNING338
macos-release-x86_64WARNING616
macos-oldrel-arm64WARNING438
macos-oldrel-x86_64WARNING597
windows-develWARNING584
windows-releaseWARNING507
windows-oldrelWARNING508
wasm-releaseOK173

Exports:checkMemoryCachecolBlockApplyflushMemoryCachegetExecutorinitializeCppisFileBackedMatrixrealizeFileBackedMatrixrowBlockApplytatami.arithtatami.binarytatami.bindtatami.columntatami.column.medianstatami.column.nan.countstatami.column.sumstatami.comparetatami.dimtatami.gettatami.is.sparsetatami.logtatami.logictatami.mathtatami.medianstatami.multiplytatami.nan.countstatami.nottatami.prefer.rowstatami.realizetatami.roundtatami.rowtatami.row.medianstatami.row.nan.countstatami.row.sumstatami.subsettatami.sumstatami.sums.by.grouptatami.transposetoCsparsewhichNonZero

Dependencies:abindassortheadBiocGenericsDelayedArraygenericsIRangeslatticeMatrixMatrixGenericsmatrixStatsRcppS4ArraysS4VectorsSparseArrayXVector

Developing packages with beachmat

Aaron Lun

Rendered fromlinking.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2025-08-19
Started: 2018-03-13

Readme and manuals

Help Manual

Help pageTopics
Check the in-memory cache for matrix instancescheckMemoryCache flushMemoryCache
Apply over blocks of columns or rowscolBlockApply rowBlockApply
Get the parallel executorgetExecutor
Initialize matrix in C++ memory spaceinitializeCpp initializeCpp,ANY-method initializeCpp,ConstantArraySeed-method initializeCpp,DelayedAbind-method initializeCpp,DelayedAperm-method initializeCpp,DelayedMatrix-method initializeCpp,DelayedNaryIsoOp-method initializeCpp,DelayedSetDimnames-method initializeCpp,DelayedSubset-method initializeCpp,DelayedUnaryIsoOpStack-method initializeCpp,DelayedUnaryIsoOpWithArgs-method initializeCpp,dgCMatrix-method initializeCpp,dgeMatrix-method initializeCpp,dgRMatrix-method initializeCpp,externalptr-method initializeCpp,lgCMatrix-method initializeCpp,lgeMatrix-method initializeCpp,lgRMatrix-method initializeCpp,matrix-method initializeCpp,SVT_SparseMatrix-method
Realize a file-backed DelayedMatrixisFileBackedMatrix realizeFileBackedMatrix
Tatami utilitiestatami-utils tatami.arith tatami.binary tatami.bind tatami.column.medians tatami.column.nan.counts tatami.column.sums tatami.compare tatami.dim tatami.get tatami.is.sparse tatami.log tatami.logic tatami.math tatami.medians tatami.multiply tatami.nan.counts tatami.not tatami.prefer.rows tatami.realize tatami.round tatami.row.medians tatami.row.nan.counts tatami.row.sums tatami.subset tatami.sums tatami.sums.by.group tatami.transpose
Convert a SparseMatrix to a CsparseMatrixtoCsparse
Find non-zero entries of a matrixwhichNonZero