DOI: 10.18129/B9.bioc.scater    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see scater.

Single-Cell Analysis Toolkit for Gene Expression Data in R

Bioconductor version: 3.8

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, cre], Kieran Campbell [aut], Aaron Lun [aut, ctb], Quin Wills [aut], Vladimir Kiselev [ctb]

Maintainer: Davis McCarthy <davis at>

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


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HTML R Script An introduction to the scater package
HTML R Script Data visualisation methods in scater
HTML R Script Quality control with scater
PDF   Reference Manual
Text   NEWS


biocViews Coverage, DataImport, DataRepresentation, DimensionReduction, GeneExpression, ImmunoOncology, Infrastructure, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.10.1
In Bioconductor since BioC 3.3 (R-3.3) (3 years)
License GPL-3
Depends R (>= 3.5), SingleCellExperiment, ggplot2, BiocParallel
Imports BiocGenerics, SummarizedExperiment, Matrix, dplyr, ggbeeswarm, grid, DelayedMatrixStats, methods, plyr, reshape2, S4Vectors, stats, utils, viridis, Rcpp (>= 0.12.14), DelayedArray
LinkingTo Rhdf5lib, Rcpp, beachmat
Suggests BiocStyle, biomaRt, beachmat, cowplot, cluster, destiny, knitr, monocle, mvoutlier, rmarkdown, Rtsne, umap, testthat, magrittr, pheatmap, irlba, tximport, tximportData, tximeta, Biobase, limma
SystemRequirements C++11
Depends On Me netSmooth, simpleSingleCell
Imports Me CATALYST, scran, splatter
Suggests Me CellTrails, DuoClustering2018, iSEE, MAST, monocle, SC3, slalom, SummarizedBenchmark, TabulaMurisData
Links To Me
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Source Package scater_1.10.1.tar.gz
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Mac OS X 10.11 (El Capitan) scater_1.10.1.tgz
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