scater

This is the released version of scater; for the devel version, see scater.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3

Single-Cell Analysis Toolkit for Gene Expression Data in R

Bioconductor version: Release (3.23)

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] ORCID: 0000-0001-5537-637X , Tuomas Borman [ctb] ORCID: 0000-0002-8563-8884

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

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

Davis McCarthy, Kieran Campbell, Aaron Lun, Quin Wills. scater: Single-Cell Analysis Toolkit for Gene Expression Data in R. doi:10.18129/B9.bioc.scater, R package version 1.40.2, https://bioconductor.org/packages/scater.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("scater")

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

Documentation

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

browseVignettes("scater")

Single-cell analysis toolkit for expression in R	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Coverage, DataImport, DataRepresentation, DimensionReduction, GeneExpression, ImmunoOncology, Infrastructure, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version	1.40.2
In Bioconductor since	BioC 3.3 (R-3.3) (10.5 years)
License	GPL-3
Depends	SingleCellExperiment, scuttle, ggplot2
Imports	stats, utils, methods, Matrix, BiocGenerics, S4Vectors, SummarizedExperiment, MatrixGenerics, SparseArray, DelayedArray, beachmat, BiocNeighbors, BiocSingular, BiocParallel, rlang, ggbeeswarm, viridis, Rtsne, RColorBrewer, RcppML, uwot, pheatmap, ggrepel
System Requirements
URL	http://bioconductor.org/packages/scater/
Bug Reports	https://support.bioconductor.org/

Suggests	BiocStyle, DelayedMatrixStats, snifter, densvis, cowplot, biomaRt, knitr, scRNAseq, robustbase, rmarkdown, testthat, Biobase, scattermore, ggrastr, MASS
Linking To
Enhances
Depends On Me	chevreulProcess, netSmooth, omicsGMF
Imports Me	airpart, BayesSpace, blase, CAESAR.Suite, CATALYST, celda, CelliD, CellMixS, chevreulPlot, ChromSCape, clustSIGNAL, decontX, distinct, DoReMiTra, epiregulon.extra, FLAMES, M3Drop, MEB, mia, miaDash, miaViz, muscat, peco, pipeComp, PRECAST, RegionalST, scDblFinder, scDotPlot, scMerge, scTreeViz, scviR, shinyDSP, singleCellTK, SpaceTrooper, Spaniel, spatialLIBD, tricycle, VAExprs
Suggests Me	alabaster.sfe, anglemania, APL, Banksy, BatChef, batchelor, bluster, Canek, ccImpute, CellMentor, CellTrails, Cepo, CiteFuse, coFAST, concordexR, Coralysis, corral, crumblr, curatedMetagenomicData, dandelionR, DeeDeeExperiment, dittoSeq, DOtools, dreamlet, DuoClustering2018, epiregulon, escheR, ExperimentSubset, futurize, ggsc, ggspavis, Glimma, GSABenchmark, hammers, harf, HCAData, HCATonsilData, HoloFoodR, HVP, Ibex, immLynx, InteractiveComplexHeatmap, iSEE, iSEEfier, iSEEhex, iSEEpathways, iSEEtree, iSEEu, jazzPanda, MAST, mbkmeans, MerfishData, MGnifyR, miaTime, miloR, miQC, monocle, MOSim, MouseAgingData, msqrob2, MuData, mumosa, muscData, Nebulosa, ProFAST, raer, ReactomeGSA, SanityR, SC3, SCArray, scDiagnostics, scds, scellpam, scGraphVerse, schex, scHOT, scLANE, scLang, scone, scp, scPipe, scran, scrapper, scRepertoire, Seqtometry, simPIC, simpleSingleCell, SingleCellAlleleExperiment, SingleCellMultiModal, sketchR, slalom, smartid, smoothclust, SpaNorm, SpatialFeatureExperiment, spatialHeatmap, speckle, splatter, SPOTlight, StabMap, standR, SuperCell, SuperCellCyto, SVP, TabulaMurisData, tidySingleCellExperiment, tidySpatialExperiment, tuberculosis, UCell, velociraptor, Voyager, waddR
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	scater_1.40.2.tar.gz
Windows Binary (x86_64)	scater_1.40.2.zip
macOS Binary (big-sur-x86_64)	scater_1.40.2.tgz
macOS Binary (sonoma-arm64)	scater_1.40.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scater
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scater
Package Short Url	https://bioconductor.org/packages/scater/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.23	Source Archive