Package: BPCellsArray 0.0.0.9000

BPCellsArray: Using BPCells as a DelayedArray Backend

Implements a DelayedArray backend for reading and writing arrays in the BPCells storage layout. The resulting BPCells*Arrays are compatible with all Bioconductor pipelines that can accept DelayedArray instances.

Authors:Yun Peng [aut, cre]

BPCellsArray_0.0.0.9000.tar.gz
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BPCellsArray.pdf |BPCellsArray.html✨
BPCellsArray/json (API)

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

Bug tracker:https://github.com/yunuuuu/bpcellsarray/issues

On CRAN:

Conda:

softwaredataimportdatarepresentationinfrastructuresingle-cell

4.32 score 7 stars 75 exports 33 dependencies

Last updated 8 months agofrom:914ae0ad8c. Checks:1 OK, 8 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 21 2025
R-4.5-winNOTEMar 21 2025
R-4.5-macNOTEMar 21 2025
R-4.5-linuxNOTEMar 21 2025
R-4.4-winNOTEMar 21 2025
R-4.4-macNOTEMar 21 2025
R-4.4-linuxNOTEMar 21 2025
R-4.3-winNOTEMar 21 2025
R-4.3-macNOTEMar 21 2025

Exports:acbindapermapplyarbindArithas.arrayas.matrixbinarizebindCOLSbindROWSBPCellsArrayBPCellsMatrixBPCellsSeedcbindcbind2chunkdimcolMaxscolMeanscolnames<-colRankscolSdscolSumscolVarsCompareconvert_modeDelayedArrayexpm1_slowextract_arrayextract_sparse_arrayis_noopis_sparselog1p_singlemask_matrixMathMath2matrix_statsmatrixClassOLD_extract_sparse_arrayOpspmax2pmin_by_colpmin_by_rowpmin_scalarpmin2rank_transformrbindrbind2readBPCells10xHDF5MatrixreadBPCellsAnnHDF5MatrixreadBPCellsDirMatrixreadBPCellsHDF5MatrixrowMaxsrowMeansrownames<-rowRanksrowSdsrowSumsrowVarsrunSVDseedApplyset_threadsshowshowtreeSpectraParamstorage_axisstorage_modettranspose_axistypetype<-writeBPCells10xHDF5MatrixwriteBPCellsAnnHDF5MatrixwriteBPCellsDirMatrixwriteBPCellsHDF5MatrixwriteBPCellsMemMatrix

Dependencies:abindassortheadbeachmatBHBiocGenericsBiocParallelBiocSingularBPCellsclicodetoolscpp11crayonDelayedArrayformatRfutile.loggerfutile.optionsgenericsIRangesirlbalambda.rlatticeMatrixMatrixGenericsmatrixStatsRcpprlangrsvdS4ArraysS4VectorsScaledMatrixsnowSparseArrayXVector

BPCells backend for DelayedArray objects

Rendered fromBPCellsArray.Rmdusingknitr::rmarkdownon Mar 21 2025.

Last update: 2024-07-10
Started: 2024-01-22

Readme and manuals

Help Manual

Help pageTopics
Apply Functions Over matrix Marginsapply apply,BPCellsMatrix-method
Arithmetic operators for BPCellsMatrixArith,BPCellsMatrix,numeric-method Arith,numeric,BPCellsMatrix-method BPCells-Arith BPCells-Arithmetic
Combine two Objects by Columns or Rowsacbind acbind,BPCellsMatrix-method arbind arbind,BPCellsMatrix-method bindCOLS bindCOLS,BPCellsMatrix-method bindROWS bindROWS,BPCellsMatrix-method BPCells-bind cbind cbind,BPCellsMatrix-method cbind2 cbind2,BPCellsMatrix,BPCellsMatrix-method rbind rbind,BPCellsMatrix-method rbind2 rbind2,BPCellsMatrix,BPCellsMatrix-method
Convert matrix elements to zeros and ones<,numeric,BPCellsMatrix-method <=,numeric,BPCellsMatrix-method >,BPCellsMatrix,numeric-method >=,BPCellsMatrix,numeric-method binarize binarize,BPCellsMatrix-method BPCells-Compare
Matrix CrossproductBPCells-crossprod crossprod crossprod,ANY,BPCellsMatrix-method crossprod,BPCellsMatrix,ANY-method crossprod,BPCellsMatrix,BPCellsMatrix-method crossprod,BPCellsMatrix,matrix-method crossprod,BPCellsMatrix,numeric-method crossprod,matrix,BPCellsMatrix-method crossprod,numeric,BPCellsMatrix-method
Math operators for BPCellsMatrixBPCells-Math expm1 expm1,BPCellsMatrix-method expm1_slow expm1_slow,BPCellsMatrix-method log1p log1p,BPCellsMatrix-method log1p_single log1p_single,BPCellsMatrix-method round round,BPCellsMatrix-method
Matrix Multiplication%*%,ANY,BPCellsMatrix-method %*%,BPCellsMatrix,ANY-method %*%,BPCellsMatrix,BPCellsMatrix-method %*%,BPCellsMatrix,matrix-method %*%,BPCellsMatrix,numeric-method %*%,matrix,BPCellsMatrix-method %*%,numeric,BPCellsMatrix-method BPCells-Multiplication
BPCellsMatrix row/col summarizationBPCells-Summarization colMaxs colMaxs,BPCellsMatrix-method colMeans colMeans,BPCellsMatrix-method colSds colSds,BPCellsMatrix-method colSums colSums,BPCellsMatrix-method colVars colVars,BPCellsMatrix-method matrix_stats matrix_stats,BPCellsMatrix-method rowMaxs rowMaxs,BPCellsMatrix-method rowMeans rowMeans,BPCellsMatrix-method rowSds rowSds,BPCellsMatrix-method rowSums rowSums,BPCellsMatrix-method rowVars rowVars,BPCellsMatrix-method
Matrix Products of TransposeBPCells-tcrossprod tcrossprod tcrossprod,ANY,BPCellsMatrix-method tcrossprod,BPCellsMatrix,ANY-method tcrossprod,BPCellsMatrix,BPCellsMatrix-method tcrossprod,BPCellsMatrix,matrix-method tcrossprod,BPCellsMatrix,numeric-method tcrossprod,matrix,BPCellsMatrix-method tcrossprod,numeric,BPCellsMatrix-method
Read/write sparse matrices from (or into) 10x feature matrixBPCells10xHDF5-IO readBPCells10xHDF5Matrix writeBPCells10xHDF5Matrix writeBPCells10xHDF5Matrix,ANY-method
Read/write sparse matrices from (or into) AnnData HDF5 fileBPCellsAnnHDF5-IO readBPCellsAnnHDF5Matrix writeBPCellsAnnHDF5Matrix writeBPCellsAnnHDF5Matrix,ANY-method
BPCellsDelayedOp objectsas.array,BPCellsDelayedOp-method as.array.BPCellsDelayedOp as.matrix,BPCellsDelayedOp-method as.matrix.BPCellsDelayedOp BPCellsDelayedOp-class chunkdim,BPCellsDelayedOp-method dim,BPCellsDelayedOp-method dimnames,BPCellsDelayedOp-method extract_array,BPCellsDelayedOp-method extract_sparse_array,BPCellsDelayedOp-method is_noop,BPCellsDelayedAbind-method is_noop,BPCellsDelayedRenameDims-method is_noop,BPCellsDelayedSubset-method is_sparse,BPCellsDelayedOp-method OLD_extract_sparse_array,BPCellsDelayedOp-method t,BPCellsDelayedOp-method type,BPCellsDelayedOp-method
Read/write sparse matrices from (or into) directory on diskBPCellsDir-IO readBPCellsDirMatrix writeBPCellsDirMatrix writeBPCellsDirMatrix,ANY-method
Read/write sparse matrices from (or into) HDF5 fileBPCellsHDF5-IO readBPCellsHDF5Matrix writeBPCellsHDF5Matrix writeBPCellsHDF5Matrix,ANY-method
Write a sparce matrices into memory with BPCells formatBPCellsMem-IO writeBPCellsMemMatrix writeBPCellsMemMatrix,ANY-method
Transform into 'IterableMatrix'BPCellsSeed BPCellsSeed,ANY-method BPCellsSeed,dgCMatrix-method BPCellsSeed,IterableMatrix-method BPCellsSeed,matrix-method
'IterableMatrix' object methodsas.array,IterableMatrix-method as.array.IterableMatrix BPCellsSeed-class chunkdim,IterableMatrix-method extract_array,IterableMatrix-method extract_sparse_array,IterableMatrix-method is_sparse,IterableMatrix-method IterableMatrix OLD_extract_sparse_array,IterableMatrix-method type,IterableMatrix-method
Convert the storage mode of a BPCellsArray objectconvert_mode convert_mode,BPCellsMatrix-method storage_mode storage_mode,BPCellsDelayedOp-method storage_mode,BPCellsMatrix-method storage_mode,IterableMatrix-method storage_mode,matrix-method
House of internal methods%%,BPCellsMatrix,numeric-method %%,numeric,BPCellsMatrix-method %/%,BPCellsMatrix,numeric-method %/%,numeric,BPCellsMatrix-method /,numeric,BPCellsMatrix-method binarize,ANY-method BPCellsSeed,BPCellsMatrix-method cbind2,ANY,BPCellsMatrix-method cbind2,BPCellsMatrix,ANY-method Compare,ANY,BPCellsMatrix-method Compare,BPCellsMatrix,ANY-method convert_mode,ANY-method DelayedArray,BPCellsDelayedOp-method expm1_slow,ANY-method internal-methods log,BPCellsMatrix-method mask_matrix,ANY,ANY-method Math,BPCellsArray-method Math2,BPCellsArray-method pmax2,BPCellsMatrix,DelayedArray-method pmax2,BPCellsMatrix,vector-method pmax2,DelayedArray,BPCellsMatrix-method pmax2,vector,BPCellsMatrix-method pmin2,BPCellsMatrix,DelayedArray-method pmin2,BPCellsMatrix,vector-method pmin2,DelayedArray,BPCellsMatrix-method pmin2,vector,BPCellsMatrix-method rank_transform,ANY-method rbind2,ANY,BPCellsMatrix-method rbind2,BPCellsMatrix,ANY-method set_threads,ANY-method set_threads,BPCellsDelayedAbind-method set_threads,ColBindMatrices-method set_threads,RowBindMatrices-method transpose_axis,ANY-method [<-,BPCellsMatrix,ANY,ANY,dgCMatrix-method [<-,BPCellsMatrix,ANY,ANY,matrix-method
Mask matrix entries to zeromask_matrix mask_matrix,BPCellsMatrix,ANY-method mask_matrix,BPCellsMatrix,BPCellsMatrix-method
Maxima and Minimapmax2 pmin2 pmin2,BPCellsMatrix,numeric-method pmin2,numeric,BPCellsMatrix-method pmin_by_col pmin_by_col,BPCellsMatrix-method pmin_by_row pmin_by_row,BPCellsMatrix-method pmin_scalar pmin_scalar,BPCellsMatrix-method
Rank-transform a BPCells IterableMatrix matrixcolRanks colRanks,BPCellsMatrix-method rank_transform rank_transform,BPCellsMatrix-method rowRanks rowRanks,BPCellsMatrix-method
Set matrix op thread countset_threads set_threads,BPCellsMatrix-method
DelayedArray backend of BPCells matrixaperm,BPCellsMatrix-method aperm.BPCellsMatrix as.array,BPCellsMatrix-method as.array.BPCellsMatrix as.matrix,BPCellsMatrix-method as.matrix.BPCellsMatrix BPCellsArray BPCellsArray-class BPCellsMatrix BPCellsMatrix-class BPCellsMatrix-methods colnames<- colnames<-,BPCellsMatrix-method DelayedArray,IterableMatrix-method dimnames<- dimnames<-,BPCellsMatrix,ListOrNULL-method is.finite,BPCellsMatrix-method is.infinite,BPCellsMatrix-method is.na,BPCellsMatrix-method is.nan,BPCellsMatrix-method matrixClass,BPCellsArray-method Ops,BPCellsArray,BPCellsArray-method Ops,BPCellsArray,vector-method Ops,vector,BPCellsArray-method rownames<- rownames<-,BPCellsMatrix-method show,BPCellsArray-method show,BPCellsMatrix-method t t,BPCellsMatrix-method type<-,BPCellsMatrix-method [,BPCellsMatrix,ANY,ANY,ANY-method [<-,BPCellsMatrix,ANY,ANY,ANY-method [<-,BPCellsMatrix,ANY,ANY,BPCellsMatrix-method [<-,BPCellsMatrix,ANY,ANY,IterableMatrix-method
Visualize and access the leaves of a tree of delayed operationsseedApply showtree
BiocSingularParam classesrunSVD,SpectraParam-method SpectraParam SpectraParam-class
Transpose the storage axis for a 'BPCellsSeed' or 'BPCellsMatrix' objectstorage_axis storage_axis,BPCellsDelayedOp-method storage_axis,BPCellsMatrix-method storage_axis,IterableMatrix-method transpose_axis transpose_axis,BPCellsMatrix-method