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Single-Cell Analysis Toolkit for Gene Expression Data in R

Bioconductor version: Release (3.19)

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

Author: 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]

Maintainer: Alan O'Callaghan <alan.ocallaghan at>

Citation (from within R, enter citation("scater")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Overview of scater functionality HTML R Script
Reference Manual PDF


biocViews Coverage, DataImport, DataRepresentation, DimensionReduction, GeneExpression, ImmunoOncology, Infrastructure, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.32.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License GPL-3
Depends SingleCellExperiment, scuttle, ggplot2
Imports stats, utils, methods, Matrix, BiocGenerics, S4Vectors, SummarizedExperiment, DelayedArray, MatrixGenerics, beachmat, BiocNeighbors, BiocSingular, BiocParallel, rlang, ggbeeswarm, viridis, Rtsne, RColorBrewer, RcppML, uwot, pheatmap, ggrepel, ggrastr
System Requirements
Bug Reports
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Suggests BiocStyle, snifter, densvis, cowplot, biomaRt, knitr, scRNAseq, robustbase, rmarkdown, testthat, Biobase, scattermore
Linking To
Depends On Me netSmooth, OSCA.advanced, OSCA.basic, OSCA.intro, OSCA.multisample, OSCA.workflows, SingleRBook
Imports Me airpart, BayesSpace, CATALYST, celda, CelliD, CellMixS, ChromSCape, decontX, distinct, epiregulon.extra, FLAMES, M3Drop, MEB, mia, miaViz, muscat, peco, pipeComp, RegionalST, scDblFinder, scMerge, scTreeViz, scviR, singleCellTK, Spaniel, spatialHeatmap, tricycle, VAExprs, spatialLIBD, PRECAST, SC.MEB
Suggests Me APL, Banksy, batchelor, bluster, ccImpute, CellTrails, Cepo, CiteFuse, concordexR, corral, dittoSeq, dreamlet, epiregulon, escheR, ExperimentSubset, ggsc, ggspavis, Glimma, InteractiveComplexHeatmap, iSEE, iSEEfier, iSEEhex, iSEEpathways, iSEEu, MAST, mbkmeans, MGnifyR, miloR, miQC, monocle, MOSim, MuData, mumosa, Nebulosa, netDx, raer, SC3, SCArray, scds, schex, scHOT, scone, scp, scPipe, scran, scRepertoire, SingleCellAlleleExperiment, SingleR, sketchR, slalom, smartid, smoothclust, SpatialFeatureExperiment, speckle, splatter, SPOTlight, standR, tidySingleCellExperiment, tidySpatialExperiment, traviz, UCell, velociraptor, Voyager, waddR, curatedMetagenomicData, DuoClustering2018, HCAData, HCATonsilData, MouseAgingData, muscData, SingleCellMultiModal, TabulaMurisData, tuberculosis, simpleSingleCell, spicyWorkflow, Canek, ProFAST, SCdeconR, scellpam
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Source Package scater_1.32.0.tar.gz
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