Package: SCArray 1.21.2

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]

SCArray_1.21.2.tar.gz
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SCArray_1.21.2.tgz(r-4.6-x86_64)SCArray_1.21.2.tgz(r-4.6-arm64)SCArray_1.21.2.tgz(r-4.5-x86_64)SCArray_1.21.2.tgz(r-4.5-arm64)
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SCArray_1.21.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SCArray/json (API)

# 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-1.21.0(bioc 3.24)SCArray-1.20.0(bioc 3.23)

infrastructuredatarepresentationdataimportsinglecellrnaseqcpp

5.26 score 1 stars 1 packages 15 scripts 476 downloads 68 exports 37 dependencies

Last updated from:36586cf396. Checks:10 ERROR, 2 OK, 3 NOTE, 1 WARNING. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR179
linux-devel-arm64ERROR278
linux-devel-x86_64ERROR304
source / vignettesOK335
linux-release-arm64ERROR238
linux-release-x86_64ERROR366
macos-release-arm64NOTE254
macos-release-x86_64ERROR442
macos-oldrel-arm64WARNING255
macos-oldrel-x86_64ERROR499
windows-devel-arm64NOTE334
windows-devel-x86_64ERROR282
windows-release-arm64NOTE374
windows-release-x86_64ERROR295
windows-oldrel-x86_64ERROR272
wasm-releaseOK148

Exports:col_nnzerocolAnyNAscolAvgsPerRowSetcolCollapsecolDiffscolLogSumExpscolMaxscolMeanscolMeans2colMinscolProdscolRangescolSdDiffscolSdscolsumcolSumscolSums2colVarDiffscolVarscolWeightedMeanscolWeightedSdscolWeightedVarspmax2pmin2row_nnzerorowAnyNAsrowAvgsPerColSetrowCollapserowDiffsrowLogSumExpsrowMaxsrowMeansrowMeans2rowMinsrowProdsrowRangesrowSdDiffsrowSdsrowsumrowSumsrowSums2rowVarDiffsrowVarsrowWeightedMeansrowWeightedSdsrowWeightedVarsrunPCAscalescArrayscClosescColAutoGridscColMeanVarscConvGDSscExperimentscGetFilesscHDF2GDSscMemoryscMEX2GDSscNumSplitscObjscOpenscReplaceNAscRowAutoGridscRowMeanVarscRunPCAscSetBoundsscSetMaxscSetMin

Dependencies:abindassortheadbeachmatBHBiobaseBiocGenericsBiocParallelBiocSingularcodetoolscpp11DelayedArrayDelayedMatrixStatsformatRfutile.loggerfutile.optionsgdsfmtgenericsGenomicRangesIRangesirlbalambda.rlatticeMatrixMatrixGenericsmatrixStatsRcpprsvdS4ArraysS4VectorsScaledMatrixSeqinfoSingleCellExperimentsnowSparseArraysparseMatrixStatsSummarizedExperimentXVector

SCArray -- Large-scale single-cell omics data manipulation with GDS files
Introduction | Workflow & Data Structure | Key Functions in SCArray | Example: Small-size Dataset | Example: Large-size Dataset (1.3M mouse brain cells) | Discussion | Acknowledgements
Rendered fromOverview.Rmdusingknitr::rmarkdown

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

Large-scale single-cell omics data manipulation with GDS files
Introduction | Installation | Format conversion | Conversion from SingleCellExperiment | Conversion from a matrix | Examples | Data Manipulation and Analysis | 1. Row and Column Summarization | 2. PCA analysis | 3. UMAP analysis | Miscellaneous | Debugging | Session Information
Rendered fromSCArray.Rmdusingknitr::rmarkdown

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

Readme and manuals

Help Manual

Help pageTopics
Large-scale single-cell omics data manipulation with GDS filesSCArray-package SCArray
Numbers of Non-zeroscol_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 instancescArray
Class list defined in SCArraySCArray-classes SCArrayFileClass SCArrayFileClass-class SC_GDSArray SC_GDSArray-class SC_GDSMatrix SC_GDSMatrix-class
SC_GDSMatrix row/column summarizationcolAnyNAs 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 filescConvGDS
Get a SummarizedExperimentscExperiment
File names for on-disk backendscGetFiles scGetFiles,SC_GDSArray-method scGetFiles,SummarizedExperiment-method
Convert HDF5 files to GDSscHDF2GDS
Load Data to MemoryscMemory scMemory,DelayedArray-method scMemory,SummarizedExperiment-method
Convert MEX files to GDSscMEX2GDS
Split a numberscNumSplit
DelayedArray Object in GDSscObj
Open/Close a Single-cell GDS FilescClose scOpen
ReplacementscReplaceNA
Automatic grids for matrix-like objectsscColAutoGrid scRowAutoGrid
Perform PCA on SC_GDSMatrix and expression datarunPCA runPCA,SC_GDSMatrix-method scRunPCA
Set the boundsscSetBounds scSetMax scSetMin