Package: scater 1.33.4
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:
scater_1.33.4.tar.gz
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scater.pdf |scater.html✨
scater/json (API)
NEWS
# Install 'scater' in R: |
install.packages('scater', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
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
Last updated 3 months agofrom:d14427e677. Checks:OK: 3 NOTE: 2 ERROR: 2. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Sep 17 2024 |
R-4.5-win | NOTE | Sep 17 2024 |
R-4.5-linux | NOTE | Sep 17 2024 |
R-4.4-win | OK | Sep 17 2024 |
R-4.4-mac | ERROR | Sep 17 2024 |
R-4.3-win | OK | Sep 17 2024 |
R-4.3-mac | ERROR | Sep 17 2024 |
Exports:addPerCellQCaddPerFeatureQCaggregateAcrossCellsaggregateAcrossFeaturesannotateBMFeaturesbootstrapsbootstraps<-calculateAveragecalculateCPMcalculateDiffusionMapcalculateFPKMcalculateMDScalculateMultiUMAPcalculateNMFcalculatePCAcalculateQCMetricscalculateTPMcalculateTSNEcalculateUMAPcentreSizeFactorscomputeLibraryFactorscomputeMedianFactorsfpkmfpkm<-getBMFeatureAnnosgetExplanatoryPCsgetVarianceExplainedggcellsggfeaturesisOutlierlibrarySizeFactorslogNormCountsmakePerCellDFmakePerFeatureDFmedianSizeFactorsmockSCEmultiplotnexprsnorm_exprsnorm_exprs<-normalizenormalizeCountsnumDetectedAcrossCellsnumDetectedAcrossFeaturesperCellQCMetricsperFeatureQCMetricsplotColDataplotDiffusionMapplotDotsplotExplanatoryPCsplotExplanatoryVariablesplotExpressionplotGroupedHeatmapplotHeatmapplotHighestExprsplotMDSplotNMFplotPCAplotPCASCEplotPlatePositionplotReducedDimplotRLEplotRowDataplotScaterplotTSNEplotUMAPprojectReducedDimquickPerCellQCreadSparseCountsretrieveCellInforetrieveFeatureInforunColDataPCArunDiffusionMaprunMDSrunMultiUMAPrunNMFrunPCArunTSNErunUMAPstand_exprsstand_exprs<-sumCountsAcrossCellssumCountsAcrossFeaturestoSingleCellExperimentuniquifyFeatureNamesupdateSCESet
Dependencies:abindaskpassassortheadbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularCairoclicodetoolscolorspacecpp11crayoncurlDelayedArraydqrngfansifarverFNNformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggrastrggrepelgluegridExtragtablehttrIRangesirlbaisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpheatmappillarpkgconfigpngR6raggRColorBrewerRcppRcppAnnoyRcppEigenRcppMLRcppProgressrlangRSpectrarsvdRtsneS4ArraysS4VectorsScaledMatrixscalesscuttleSingleCellExperimentsitmosnowSparseArraySummarizedExperimentsyssystemfontstextshapingtibbleUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrXVectorzlibbioc
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Get feature annotation information from Biomart | annotateBMFeatures getBMFeatureAnnos |
Accessor and replacement for bootstrap results in a 'SingleCellExperiment' object | bootstraps bootstraps,SingleCellExperiment-method bootstraps<- bootstraps<-,SingleCellExperiment,array-method |
Perform MDS on cell-level data | calculateMDS calculateMDS,ANY-method calculateMDS,SingleCellExperiment-method calculateMDS,SummarizedExperiment-method runMDS |
Perform NMF on cell-level data | calculateNMF calculateNMF,ANY-method calculateNMF,SingleCellExperiment-method calculateNMF,SummarizedExperiment-method runNMF |
Perform PCA on expression data | calculatePCA calculatePCA,ANY-method calculatePCA,SingleCellExperiment-method calculatePCA,SummarizedExperiment-method runPCA runPCA,SingleCellExperiment-method |
Perform t-SNE on cell-level data | calculateTSNE calculateTSNE,ANY-method calculateTSNE,SingleCellExperiment-method calculateTSNE,SummarizedExperiment-method runTSNE |
Perform UMAP on cell-level data | calculateUMAP calculateUMAP,ANY-method calculateUMAP,SingleCellExperiment-method calculateUMAP,SummarizedExperiment-method runUMAP |
Defunct functions | calculateDiffusionMap calculateDiffusionMap,ANY-method calculateQCMetrics centreSizeFactors defunct multiplot normalize,SingleCellExperiment-method runDiffusionMap |
Per-PC variance explained by a variable | getExplanatoryPCs |
Per-gene variance explained by a variable | getVarianceExplained getVarianceExplained,ANY-method getVarianceExplained,SummarizedExperiment-method |
Create a ggplot from a SingleCellExperiment | ggcells ggfeatures |
Count the number of non-zero counts per cell or feature | nexprs 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 metadata | plotColData |
Create a dot plot of expression values | plotDots |
Plot the explanatory PCs for each variable | plotExplanatoryPCs |
Plot explanatory variables ordered by percentage of variance explained | plotExplanatoryVariables |
Plot expression values for all cells | plotExpression |
Plot heatmap of group-level expression averages | plotGroupedHeatmap |
Plot heatmap of gene expression values | plotHeatmap |
Plot the highest expressing features | plotHighestExprs |
Plot cells in plate positions | plotPlatePosition |
Plot reduced dimensions | plotReducedDim |
Plot relative log expression | plotRLE plotRLE,SingleCellExperiment-method |
Plot row metadata | plotRowData |
Plot an overview of expression for each cell | plotScater |
Project cells into an arbitrary dimensionality reduction space. | projectReducedDim projectReducedDim,matrix-method projectReducedDim,SummarizedExperiment-method |
Plot specific reduced dimensions | plotDiffusionMap plotMDS plotNMF plotPCA plotPCA,SingleCellExperiment-method plotPCASCE plotTSNE plotUMAP Reduced dimension plots |
Cell-based data retrieval | retrieveCellInfo |
Feature-based data retrieval | retrieveFeatureInfo |
Perform PCA on column metadata | runColDataPCA |
Multi-modal UMAP | calculateMultiUMAP calculateMultiUMAP,ANY-method calculateMultiUMAP,SingleCellExperiment-method calculateMultiUMAP,SummarizedExperiment-method runMultiUMAP |
The 'scater' package | scater-pkg |
General visualization parameters | scater-plot-args |
The "Single Cell Expression Set" (SCESet) class | SCESet SCESet-class |
Convert an SCESet object to a SingleCellExperiment object | toSingleCellExperiment updateSCESet |