Package: beachmat 2.23.5

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]

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beachmat.pdf |beachmat.html
beachmat/json (API)
NEWS

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

Peer review:

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

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

On BioConductor:beachmat-2.23.4(bioc 3.21)beachmat-2.22.0(bioc 3.20)

datarepresentationdataimportinfrastructurebioconductor-packagehuman-cell-atlasmatrix-librarycpp

11.06 score 4 stars 136 packages 21 scripts 30k downloads 3 mentions 31 exports 17 dependencies

Last updated 6 days agofrom:747ddb1104. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 16 2024
R-4.5-win-x86_64NOTEDec 16 2024
R-4.5-linux-x86_64NOTEDec 16 2024
R-4.4-win-x86_64NOTEDec 16 2024
R-4.4-mac-x86_64NOTEDec 16 2024
R-4.4-mac-aarch64NOTEDec 16 2024
R-4.3-win-x86_64NOTEDec 16 2024
R-4.3-mac-x86_64NOTEDec 16 2024
R-4.3-mac-aarch64NOTEDec 16 2024

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

Dependencies:abindassortheadBiocGenericscrayonDelayedArraygenericsIRangeslatticeMatrixMatrixGenericsmatrixStatsRcppS4ArraysS4VectorsSparseArrayXVectorzlibbioc

Developing packages with beachmat

Rendered fromlinking.Rmdusingknitr::rmarkdownon Dec 16 2024.

Last update: 2024-10-17
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
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 tatami.column.nan.counts tatami.column.sums tatami.compare tatami.dim tatami.is.sparse tatami.log tatami.logic tatami.math tatami.multiply tatami.not tatami.prefer.rows tatami.realize tatami.round tatami.row tatami.row.nan.counts tatami.row.sums tatami.subset tatami.transpose
Convert a SparseMatrix to a CsparseMatrixtoCsparse
Find non-zero entries of a matrixwhichNonZero