Package: SCArray 1.13.0

Xiuwen Zheng

SCArray: Large-scale single-cell omics data manipulation with GDS files

Provides large-scale single-cell omics data manipulation using Genomic Data Structure (GDS) files. It combines dense and sparse matrices stored in GDS files and the Bioconductor infrastructure framework (SingleCellExperiment and DelayedArray) to provide out-of-memory data storage and large-scale manipulation using the R programming language.

Authors:Xiuwen Zheng [aut, cre]

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SCArray.pdf |SCArray.html✨
SCArray/json (API)
NEWS

# Install 'SCArray' in R:

install.packages('SCArray', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/abbvie-computationalgenomics/scarray/issues

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:SCArray-1.13.0(bioc 3.20)SCArray-1.12.0(bioc 3.19)

bioconductor-package

68 exports 1.38 score 47 dependencies 1 dependents

Last updated 2 months agofrom:5df3190df4

Exports:col_nnzero colAnyNAs colAvgsPerRowSet colCollapse colDiffs colLogSumExps colMaxs colMeans colMeans2 colMins colProds colRanges colSdDiffs colSds colsum colSums colSums2 colVarDiffs colVars colWeightedMeans colWeightedSds colWeightedVars pmax2 pmin2 row_nnzero rowAnyNAs rowAvgsPerColSet rowCollapse rowDiffs rowLogSumExps rowMaxs rowMeans rowMeans2 rowMins rowProds rowRanges rowSdDiffs rowSds rowsum rowSums rowSums2 rowVarDiffs rowVars rowWeightedMeans rowWeightedSds rowWeightedVars runPCA scale scArray scClose scColAutoGrid scColMeanVar scConvGDS scExperiment scGetFiles scHDF2GDS scMemory scMEX2GDS scNumSplit scObj scOpen scReplaceNA scRowAutoGrid scRowMeanVar scRunPCA scSetBounds scSetMax scSetMin

Dependencies:abind askpass beachmat BH Biobase BiocGenerics BiocParallel BiocSingular codetools cpp11 crayon curl DelayedArray DelayedMatrixStats formatR futile.logger futile.options gdsfmt GenomeInfoDb GenomeInfoDbData GenomicRanges httr IRanges irlba jsonlite lambda.r lattice Matrix MatrixGenerics matrixStats mime openssl R6 Rcpp rsvd S4Arrays S4Vectors ScaledMatrix SingleCellExperiment snow SparseArray sparseMatrixStats SummarizedExperiment sys UCSC.utils XVector zlibbioc

SCArray -- Large-scale single-cell omics data manipulation with GDS files

Dr. Xiuwen Zheng, Genomics Research Center, AbbVie

Rendered fromOverview.Rmdusingknitr::rmarkdownon Jun 27 2024.

Last update: 2024-04-20
Started: 2022-01-24

Large-scale single-cell omics data manipulation with GDS files

Dr. Xiuwen Zheng (Genomics Research Center, AbbVie)

Rendered fromSCArray.Rmdusingknitr::rmarkdownon Jun 27 2024.

Last update: 2024-04-20
Started: 2020-11-10

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Large-scale single-cell omics data manipulation with GDS files	SCArray-package SCArray
Numbers of Non-zeros	col_nnzero col_nnzero,DelayedMatrix-method col_nnzero,Matrix-method col_nnzero,matrix-method col_nnzero,SC_GDSMatrix-method row_nnzero row_nnzero,DelayedMatrix-method row_nnzero,Matrix-method row_nnzero,matrix-method row_nnzero,SC_GDSMatrix-method
Get an DelayedArray instance	scArray
Class list defined in SCArray	SCArray-classes SCArrayFileClass SCArrayFileClass-class SC_GDSArray SC_GDSArray-class SC_GDSMatrix SC_GDSMatrix-class
SC_GDSMatrix row/column summarization	colAnyNAs colAnyNAs,SC_GDSMatrix-method colAvgsPerRowSet colAvgsPerRowSet,SC_GDSMatrix-method colCollapse colCollapse,SC_GDSMatrix-method colDiffs colDiffs,SC_GDSMatrix-method colLogSumExps colLogSumExps,SC_GDSMatrix-method colMaxs colMaxs,SC_GDSMatrix-method colMeans colMeans,SC_GDSMatrix-method colMeans2 colMeans2,SC_GDSMatrix-method colMins colMins,SC_GDSMatrix-method colProds colProds,SC_GDSMatrix-method colRanges colRanges,SC_GDSMatrix-method colSdDiffs colSdDiffs,SC_GDSMatrix-method colSds colSds,SC_GDSMatrix-method colsum colsum,SC_GDSMatrix-method colSums colSums,SC_GDSMatrix-method colSums2 colSums2,SC_GDSMatrix-method colVarDiffs colVarDiffs,SC_GDSMatrix-method colVars colVars,SC_GDSMatrix-method colWeightedMeans colWeightedMeans,SC_GDSMatrix-method colWeightedSds colWeightedSds,SC_GDSMatrix-method colWeightedVars colWeightedVars,SC_GDSMatrix-method rowAnyNAs rowAnyNAs,SC_GDSMatrix-method rowAvgsPerColSet rowAvgsPerColSet,SC_GDSMatrix-method rowCollapse rowCollapse,SC_GDSMatrix-method rowDiffs rowDiffs,SC_GDSMatrix-method rowLogSumExps rowLogSumExps,SC_GDSMatrix-method rowMaxs rowMaxs,SC_GDSMatrix-method rowMeans rowMeans,SC_GDSMatrix-method rowMeans2 rowMeans2,SC_GDSMatrix-method rowMins rowMins,SC_GDSMatrix-method rowProds rowProds,SC_GDSMatrix-method rowRanges rowRanges,SC_GDSMatrix-method rowSdDiffs rowSdDiffs,SC_GDSMatrix-method rowSds rowSds,SC_GDSMatrix-method rowsum rowsum,SC_GDSMatrix-method rowSums rowSums,SC_GDSMatrix-method rowSums2 rowSums2,SC_GDSMatrix-method rowVarDiffs rowVarDiffs,SC_GDSMatrix-method rowVars rowVars,SC_GDSMatrix-method rowWeightedMeans rowWeightedMeans,SC_GDSMatrix-method rowWeightedSds rowWeightedSds,SC_GDSMatrix-method rowWeightedVars rowWeightedVars,SC_GDSMatrix-method SCArray-stats scColMeanVar scColMeanVar,Matrix-method scColMeanVar,matrix-method scColMeanVar,SC_GDSMatrix-method scRowMeanVar scRowMeanVar,Matrix-method scRowMeanVar,matrix-method scRowMeanVar,SC_GDSMatrix-method
SC_GDSArray subsetting, Ops, Math	%% %%,ANY,SC_GDSMatrix-method %*%,SC_GDSMatrix,ANY-method + +,SC_GDSArray,missing-method - -,SC_GDSArray,missing-method crossprod crossprod,ANY,SC_GDSMatrix-method crossprod,SC_GDSMatrix,ANY-method crossprod,SC_GDSMatrix,missing-method dimnames<- dimnames<-,SC_GDSArray,ANY-method Math Math,SC_GDSArray-method names<- names<-,SC_GDSArray-method Ops Ops,SC_GDSArray-method pmax2 pmax2,SC_GDSArray,SC_GDSArray-method pmax2,SC_GDSArray,vector-method pmax2,vector,SC_GDSArray-method pmin2 pmin2,SC_GDSArray,SC_GDSArray-method pmin2,SC_GDSArray,vector-method pmin2,vector,SC_GDSArray-method scale scale,SC_GDSMatrix-method SCArray-utils tcrossprod tcrossprod,ANY,SC_GDSMatrix-method tcrossprod,SC_GDSMatrix,ANY-method tcrossprod,SC_GDSMatrix,missing-method [ [,SC_GDSArray,ANY,ANY,ANY-method [,SC_GDSArray-method [[ [[,SC_GDSArray,ANY,ANY-method [[,SC_GDSArray-method
Create a GDS file	scConvGDS
Get a SummarizedExperiment	scExperiment
File names for on-disk backend	scGetFiles scGetFiles,SC_GDSArray-method scGetFiles,SummarizedExperiment-method
Convert HDF5 files to GDS	scHDF2GDS
Load Data to Memory	scMemory scMemory,DelayedArray-method scMemory,SummarizedExperiment-method
Convert MEX files to GDS	scMEX2GDS
Split a number	scNumSplit
DelayedArray Object in GDS	scObj
Open/Close a Single-cell GDS File	scClose scOpen
Replacement	scReplaceNA
Automatic grids for matrix-like objects	scColAutoGrid scRowAutoGrid
Perform PCA on SC_GDSMatrix and expression data	runPCA runPCA,SC_GDSMatrix-method scRunPCA
Set the bounds	scSetBounds scSetMax scSetMin