Package: scater 1.33.4

Alan OCallaghan

scater: Single-Cell Analysis Toolkit for Gene Expression Data in R

A collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control and visualization.

Authors:Davis McCarthy [aut], Kieran Campbell [aut], Aaron Lun [aut, ctb], Quin Wills [aut], Vladimir Kiselev [ctb], Felix G.M. Ernst [ctb], Alan O'Callaghan [ctb, cre], Yun Peng [ctb], Leo Lahti [ctb], Tuomas Borman [ctb]

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NEWS

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

Peer review:

On BioConductor:scater-1.33.4(bioc 3.20)scater-1.32.1(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncologysinglecellrnaseqqualitycontrolpreprocessingnormalizationvisualizationdimensionreductiontranscriptomicsgeneexpressionsequencingsoftwaredataimportdatarepresentationinfrastructurecoverage

86 exports 11.04 score 95 dependencies 41 dependents 79 mentions 10.3k scripts 12.5k downloads

Last updated 3 months agofrom:d14427e677. Checks:OK: 3 NOTE: 2 ERROR: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 17 2024
R-4.5-winNOTESep 17 2024
R-4.5-linuxNOTESep 17 2024
R-4.4-winOKSep 17 2024
R-4.4-macERRORSep 17 2024
R-4.3-winOKSep 17 2024
R-4.3-macERRORSep 17 2024

Exports:addPerCellQCaddPerFeatureQCaggregateAcrossCellsaggregateAcrossFeaturesannotateBMFeaturesbootstrapsbootstraps<-calculateAveragecalculateCPMcalculateDiffusionMapcalculateFPKMcalculateMDScalculateMultiUMAPcalculateNMFcalculatePCAcalculateQCMetricscalculateTPMcalculateTSNEcalculateUMAPcentreSizeFactorscomputeLibraryFactorscomputeMedianFactorsfpkmfpkm<-getBMFeatureAnnosgetExplanatoryPCsgetVarianceExplainedggcellsggfeaturesisOutlierlibrarySizeFactorslogNormCountsmakePerCellDFmakePerFeatureDFmedianSizeFactorsmockSCEmultiplotnexprsnorm_exprsnorm_exprs<-normalizenormalizeCountsnumDetectedAcrossCellsnumDetectedAcrossFeaturesperCellQCMetricsperFeatureQCMetricsplotColDataplotDiffusionMapplotDotsplotExplanatoryPCsplotExplanatoryVariablesplotExpressionplotGroupedHeatmapplotHeatmapplotHighestExprsplotMDSplotNMFplotPCAplotPCASCEplotPlatePositionplotReducedDimplotRLEplotRowDataplotScaterplotTSNEplotUMAPprojectReducedDimquickPerCellQCreadSparseCountsretrieveCellInforetrieveFeatureInforunColDataPCArunDiffusionMaprunMDSrunMultiUMAPrunNMFrunPCArunTSNErunUMAPstand_exprsstand_exprs<-sumCountsAcrossCellssumCountsAcrossFeaturestoSingleCellExperimentuniquifyFeatureNamesupdateSCESet

Dependencies:abindaskpassassortheadbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularCairoclicodetoolscolorspacecpp11crayoncurlDelayedArraydqrngfansifarverFNNformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggrastrggrepelgluegridExtragtablehttrIRangesirlbaisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpheatmappillarpkgconfigpngR6raggRColorBrewerRcppRcppAnnoyRcppEigenRcppMLRcppProgressrlangRSpectrarsvdRtsneS4ArraysS4VectorsScaledMatrixscalesscuttleSingleCellExperimentsitmosnowSparseArraySummarizedExperimentsyssystemfontstextshapingtibbleUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrXVectorzlibbioc

Single-cell analysis toolkit for expression in R

Rendered fromoverview.Rmdusingknitr::rmarkdownon Sep 17 2024.

Last update: 2022-02-21
Started: 2019-07-31

Readme and manuals

Help Manual

Help pageTopics
Get feature annotation information from BiomartannotateBMFeatures getBMFeatureAnnos
Accessor and replacement for bootstrap results in a 'SingleCellExperiment' objectbootstraps bootstraps,SingleCellExperiment-method bootstraps<- bootstraps<-,SingleCellExperiment,array-method
Perform MDS on cell-level datacalculateMDS calculateMDS,ANY-method calculateMDS,SingleCellExperiment-method calculateMDS,SummarizedExperiment-method runMDS
Perform NMF on cell-level datacalculateNMF calculateNMF,ANY-method calculateNMF,SingleCellExperiment-method calculateNMF,SummarizedExperiment-method runNMF
Perform PCA on expression datacalculatePCA calculatePCA,ANY-method calculatePCA,SingleCellExperiment-method calculatePCA,SummarizedExperiment-method runPCA runPCA,SingleCellExperiment-method
Perform t-SNE on cell-level datacalculateTSNE calculateTSNE,ANY-method calculateTSNE,SingleCellExperiment-method calculateTSNE,SummarizedExperiment-method runTSNE
Perform UMAP on cell-level datacalculateUMAP calculateUMAP,ANY-method calculateUMAP,SingleCellExperiment-method calculateUMAP,SummarizedExperiment-method runUMAP
Defunct functionscalculateDiffusionMap calculateDiffusionMap,ANY-method calculateQCMetrics centreSizeFactors defunct multiplot normalize,SingleCellExperiment-method runDiffusionMap
Per-PC variance explained by a variablegetExplanatoryPCs
Per-gene variance explained by a variablegetVarianceExplained getVarianceExplained,ANY-method getVarianceExplained,SummarizedExperiment-method
Create a ggplot from a SingleCellExperimentggcells ggfeatures
Count the number of non-zero counts per cell or featurenexprs nexprs,ANY-method nexprs,SummarizedExperiment-method
Additional accessors for the typical elements of a SingleCellExperiment object.exprs exprs,SingleCellExperiment-method, exprs<-,SingleCellExperiment,ANY-method fpkm fpkm,SingleCellExperiment-method fpkm<- fpkm<-,SingleCellExperiment,ANY-method norm_exprs norm_exprs,SingleCellExperiment-method norm_exprs<- norm_exprs<-,SingleCellExperiment,ANY-method stand_exprs stand_exprs,SingleCellExperiment-method, stand_exprs<- stand_exprs<-,SingleCellExperiment,ANY-method
Plot column metadataplotColData
Create a dot plot of expression valuesplotDots
Plot the explanatory PCs for each variableplotExplanatoryPCs
Plot explanatory variables ordered by percentage of variance explainedplotExplanatoryVariables
Plot expression values for all cellsplotExpression
Plot heatmap of group-level expression averagesplotGroupedHeatmap
Plot heatmap of gene expression valuesplotHeatmap
Plot the highest expressing featuresplotHighestExprs
Plot cells in plate positionsplotPlatePosition
Plot reduced dimensionsplotReducedDim
Plot relative log expressionplotRLE plotRLE,SingleCellExperiment-method
Plot row metadataplotRowData
Plot an overview of expression for each cellplotScater
Project cells into an arbitrary dimensionality reduction space.projectReducedDim projectReducedDim,matrix-method projectReducedDim,SummarizedExperiment-method
Plot specific reduced dimensionsplotDiffusionMap plotMDS plotNMF plotPCA plotPCA,SingleCellExperiment-method plotPCASCE plotTSNE plotUMAP Reduced dimension plots
Cell-based data retrievalretrieveCellInfo
Feature-based data retrievalretrieveFeatureInfo
Perform PCA on column metadatarunColDataPCA
Multi-modal UMAPcalculateMultiUMAP calculateMultiUMAP,ANY-method calculateMultiUMAP,SingleCellExperiment-method calculateMultiUMAP,SummarizedExperiment-method runMultiUMAP
The 'scater' packagescater-pkg
General visualization parametersscater-plot-args
The "Single Cell Expression Set" (SCESet) classSCESet SCESet-class
Convert an SCESet object to a SingleCellExperiment objecttoSingleCellExperiment updateSCESet