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Single-Cell Analysis Toolkit for Gene Expression Data in R

Bioconductor version: Release (3.18)

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 outlook.com>

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


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


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


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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 1.30.1
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
URL http://bioconductor.org/packages/scater/
Bug Reports https://support.bioconductor.org/
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Suggests BiocStyle, snifter, densvis, cowplot, biomaRt, knitr, scRNAseq, robustbase, rmarkdown, testthat, Biobase, scattermore
Linking To
Depends On Me netSmooth
Imports Me airpart, BayesSpace, CATALYST, celda, CelliD, CellMixS, ChromSCape, decontX, distinct, FLAMES, IRISFGM, MEB, mia, miaViz, muscat, peco, pipeComp, RegionalST, scDblFinder, scMerge, scTreeViz, scviR, singleCellTK, Spaniel, spatialHeatmap, spatialLIBD, tricycle, VAExprs
Suggests Me APL, batchelor, bluster, ccImpute, CellaRepertorium, CellTrails, Cepo, CiteFuse, concordexR, corral, curatedMetagenomicData, dittoSeq, dreamlet, DuoClustering2018, escheR, ExperimentSubset, fcoex, ggsc, ggspavis, Glimma, HCAData, HCATonsilData, InteractiveComplexHeatmap, iSEE, iSEEhex, iSEEpathways, iSEEu, M3Drop, MAST, mbkmeans, miloR, miQC, monocle, MuData, mumosa, muscData, Nebulosa, netDx, raer, SC3, SCArray, scds, schex, scHOT, scone, scp, scPipe, scran, scRepertoire, simpleSingleCell, SingleCellMultiModal, SingleR, slalom, speckle, spicyWorkflow, splatter, SPOTlight, standR, SummarizedBenchmark, TabulaMurisData, tidySingleCellExperiment, traviz, tuberculosis, UCell, velociraptor, Voyager, waddR
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Follow Installation instructions to use this package in your R session.

Source Package scater_1.30.1.tar.gz
Windows Binary scater_1.30.1.zip
macOS Binary (x86_64) scater_1.30.1.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/scater
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scater
Bioc Package Browser https://code.bioconductor.org/browse/scater/
Package Short Url https://bioconductor.org/packages/scater/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive