Package: SCArray.sat 1.5.0
Xiuwen Zheng
SCArray.sat: Large-scale single-cell RNA-seq data analysis using GDS files and Seurat
Extends the Seurat classes and functions to support Genomic Data Structure (GDS) files as a DelayedArray backend for data representation. It relies on the implementation of GDS-based DelayedMatrix in the SCArray package to represent single cell RNA-seq data. The common optimized algorithms leveraging GDS-based and single cell-specific DelayedMatrix (SC_GDSMatrix) are implemented in the SCArray package. SCArray.sat introduces a new SCArrayAssay class (derived from the Seurat Assay), which wraps raw counts, normalized expressions and scaled data matrix based on GDS-specific DelayedMatrix. It is designed to integrate seamlessly with the Seurat package to provide common data analysis in the SeuratObject-based workflow. Compared with Seurat, SCArray.sat significantly reduces the memory usage without downsampling and can be applied to very large datasets.
Authors:
SCArray.sat_1.5.0.tar.gz
SCArray.sat_1.5.0.zip(r-4.5)SCArray.sat_1.5.0.zip(r-4.4)SCArray.sat_1.5.0.zip(r-4.3)
SCArray.sat_1.5.0.tgz(r-4.4-any)SCArray.sat_1.5.0.tgz(r-4.3-any)
SCArray.sat_1.5.0.tar.gz(r-4.5-noble)SCArray.sat_1.5.0.tar.gz(r-4.4-noble)
SCArray.sat_1.5.0.tgz(r-4.4-emscripten)SCArray.sat_1.3.2.tgz(r-4.3-emscripten)
SCArray.sat.pdf |SCArray.sat.html✨
SCArray.sat/json (API)
NEWS
| # Install 'SCArray.sat' in R: |
| install.packages('SCArray.sat', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/abbvie-computationalgenomics/scarray/issues
On BioConductor:SCArray.sat-1.5.0(bioc 3.20)SCArray.sat-1.4.0(bioc 3.19)
Last updated 2 months agofrom:17b97a4cf1
Exports:CreateAssayObject2scGetFilesscMemoryscNewAssayGDSscNewSeuratGDSsubset.SCArrayAssay
Dependencies:abindaskpassbase64encbeachmatBHBiobaseBiocGenericsBiocParallelBiocSingularbitopsbslibcachemcaToolscliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDelayedArrayDelayedMatrixStatsdeldirdigestdotCall64dplyrdqrngevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomeformatRfsfutile.loggerfutile.optionsfuturefuture.applygdsfmtgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleidenlifecyclelistenvlmtestmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectrarsvdRtsneS4ArraysS4VectorssassScaledMatrixscalesSCArrayscattermoresctransformSeuratSeuratObjectshinySingleCellExperimentsitmosnowsourcetoolsspspamSparseArraysparseMatrixStatsspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.utilsstringistringrSummarizedExperimentsurvivalsystensortibbletidyrtidyselecttinytexUCSC.utilsutf8uwotvctrsviridisLitewithrxfunxtableXVectoryamlzlibbioczoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Large-scale single-cell RNA-seq data analysis using GDS files and Seurat | SCArray.sat-package SCArray.sat |
| Create an Assay object | CreateAssayObject2 |
| Normalize Count Data | NormalizeData NormalizeData.SC_GDSMatrix |
| Run PCA | RunPCA RunPCA.SCArrayAssay RunPCA.SC_GDSMatrix |
| Scale and Center the Data | ScaleData ScaleData.SC_GDSMatrix |
| GDS-specific Assay Class | SCArrayAssay SCArrayAssay-class |
| SCArrayAssay S3 methods | GetAssayData GetAssayData.SCArrayAssay SCArrayAssay-methods SetAssayData SetAssayData.SCArrayAssay subset subset.SCArrayAssay |
| File names for on-disk backend | scGetFiles scGetFiles,Assay-method scGetFiles,SCArrayAssay-method scGetFiles,Seurat-method |
| Load Data to Memory | scMemory scMemory,SCArrayAssay-method scMemory,Seurat-method scMemory,Seurat_g-method |
| Create Assay Object | scNewAssayGDS |
| Create Seurat Object | scNewSeuratGDS |
| GDS-based Seurat Class | Seurat_g Seurat_g-class |
