Package: scater 1.35.0

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'))

On BioConductor:scater-1.35.0(bioc 3.21)scater-1.34.0(bioc 3.20)

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

immunooncology singlecell rnaseq qualitycontrol preprocessing normalization visualization dimensionreduction transcriptomics geneexpression sequencing software dataimport datarepresentation infrastructure coverage

11.05 score 40 packages 12k scripts 12k downloads 79 mentions 86 exports 96 dependencies

Last updated 2 months agofrom:7211adabdf. Checks:OK: 3 NOTE: 2 ERROR: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 30 2024
R-4.5-win	NOTE	Nov 30 2024
R-4.5-linux	NOTE	Nov 30 2024
R-4.4-win	OK	Nov 30 2024
R-4.4-mac	ERROR	Nov 30 2024
R-4.3-win	OK	Nov 30 2024
R-4.3-mac	ERROR	Nov 30 2024

Exports:addPerCellQC addPerFeatureQC aggregateAcrossCells aggregateAcrossFeatures annotateBMFeatures bootstraps bootstraps<-calculateAverage calculateCPM calculateDiffusionMap calculateFPKM calculateMDS calculateMultiUMAP calculateNMF calculatePCA calculateQCMetrics calculateTPM calculateTSNE calculateUMAP centreSizeFactors computeLibraryFactors computeMedianFactors fpkm fpkm<-getBMFeatureAnnos getExplanatoryPCs getVarianceExplained ggcells ggfeatures isOutlier librarySizeFactors logNormCounts makePerCellDF makePerFeatureDF medianSizeFactors mockSCE multiplot nexprs norm_exprs norm_exprs<-normalize normalizeCounts numDetectedAcrossCells numDetectedAcrossFeatures perCellQCMetrics perFeatureQCMetrics plotColData plotDiffusionMap plotDots plotExplanatoryPCs plotExplanatoryVariables plotExpression plotGroupedHeatmap plotHeatmap plotHighestExprs plotMDS plotNMF plotPCA plotPCASCE plotPlatePosition plotReducedDim plotRLE plotRowData plotScater plotTSNE plotUMAP projectReducedDim quickPerCellQC readSparseCounts retrieveCellInfo retrieveFeatureInfo runColDataPCA runDiffusionMap runMDS runMultiUMAP runNMF runPCA runTSNE runUMAP stand_exprs stand_exprs<-sumCountsAcrossCells sumCountsAcrossFeatures toSingleCellExperiment uniquifyFeatureNames updateSCESet

Dependencies:abind askpass assorthead beachmat beeswarm BH Biobase BiocGenerics BiocNeighbors BiocParallel BiocSingular Cairo cli codetools colorspace cpp11 crayon curl DelayedArray dqrng fansi farver FNN formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggbeeswarm ggplot2 ggrastr ggrepel glue gridExtra gtable httr IRanges irlba isoband jsonlite labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl pheatmap pillar pkgconfig png R6 ragg RColorBrewer Rcpp RcppAnnoy RcppEigen RcppML RcppProgress rlang RSpectra rsvd Rtsne S4Arrays S4Vectors ScaledMatrix scales scuttle SingleCellExperiment sitmo snow SparseArray SummarizedExperiment sys systemfonts textshaping tibble UCSC.utils utf8 uwot vctrs vipor viridis viridisLite withr XVector zlibbioc

Single-cell analysis toolkit for expression in R

Davis McCarthy, Aaron Lun

Rendered fromoverview.Rmdusingknitr::rmarkdownon Nov 30 2024.

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

Citation

Development and contributors

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