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scater

This is thereleased version of scater; for the devel version, seescater.

Single-Cell Analysis Toolkit for Gene Expression Data in R

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DOI: 10.18129/B9.bioc.scater


Bioconductor version: Release (3.22)

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

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

Citation (from within R, entercitation("scater")):

Installation

To install this package, start R (version "4.5") and enter:

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

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

Documentation

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

browseVignettes("scater")
Overview of scater functionalityHTMLR Script
Reference ManualPDF
NEWSText

Need some help? Ask on the Bioconductor Support site!

Details

biocViewsCoverage,DataImport,DataRepresentation,DimensionReduction,GeneExpression,ImmunoOncology,Infrastructure,Normalization,Preprocessing,QualityControl,RNASeq,Sequencing,SingleCell,Software,Transcriptomics,Visualization
Version1.38.0
In Bioconductor sinceBioC 3.3 (R-3.3) (9.5 years)
LicenseGPL-3
DependsSingleCellExperiment,scuttle,ggplot2
Importsstats, utils, methods,Matrix,BiocGenerics,S4Vectors,SummarizedExperiment,MatrixGenerics,SparseArray,DelayedArray,beachmat,BiocNeighbors,BiocSingular,BiocParallel,rlang,ggbeeswarm,viridis,Rtsne,RColorBrewer,RcppML,uwot,pheatmap,ggrepel,ggrastr
System Requirements
URLhttp://bioconductor.org/packages/scater/
Bug Reportshttps://support.bioconductor.org/
See More
SuggestsBiocStyle,DelayedMatrixStats,snifter,densvis,cowplot,biomaRt,knitr,scRNAseq,robustbase,rmarkdown,testthat,Biobase,scattermore
Linking To
Enhances
Depends On MechevreulProcess,netSmooth,omicsGMF, OSCA.advanced, OSCA.basic, OSCA.intro, OSCA.multisample, OSCA.workflows, SingleRBook
Imports Meairpart,BayesSpace,blase,CATALYST,celda,CelliD,CellMixS,chevreulPlot,ChromSCape,clustSIGNAL,decontX,distinct,epiregulon.extra,FLAMES,M3Drop,MEB,mia,miaDash,miaViz,muscat,peco,pipeComp,RegionalST,scDblFinder,scDotPlot,scMerge,scTreeViz,scviR,shinyDSP,singleCellTK,SpaceTrooper,Spaniel,tricycle,VAExprs,DoReMiTra,spatialLIBD, OSTA,CAESAR.Suite,PRECAST
Suggests Mealabaster.sfe,anglemania,APL,Banksy,batchelor,bluster,ccImpute,CellTrails,Cepo,CiteFuse,concordexR,Coralysis,corral,crumblr,dandelionR,dittoSeq,DOtools,dreamlet,epiregulon,escheR,ExperimentSubset,ggsc,ggspavis,Glimma,HoloFoodR,HVP,Ibex,InteractiveComplexHeatmap,iSEE,iSEEfier,iSEEhex,iSEEpathways,iSEEtree,iSEEu,jazzPanda,MAST,mbkmeans,MGnifyR,miaTime,miloR,miQC,monocle,MOSim,MuData,mumosa,Nebulosa,raer,ReactomeGSA,SanityR,SC3,SCArray,scDiagnostics,scds,scGraphVerse,schex,scHOT,scLANE,scone,scp,scPipe,scran,scRepertoire,simPIC,SingleCellAlleleExperiment,sketchR,slalom,smartid,smoothclust,SpatialFeatureExperiment,speckle,splatter,SPOTlight,StabMap,standR,SuperCellCyto,SVP,tidySingleCellExperiment,tidySpatialExperiment,UCell,velociraptor,Voyager,waddR,curatedMetagenomicData,DuoClustering2018,HCAData,HCATonsilData,MerfishData,MouseAgingData,muscData,SingleCellMultiModal,TabulaMurisData,tuberculosis,simpleSingleCell,spicyWorkflow,Canek,coFAST,ProFAST,SCdeconR,scellpam,SuperCell
Links To Me
Build ReportBuild Report

Package Archives

FollowInstallation instructions to use this package in your R session.

Source Packagescater_1.38.0.tar.gz
Windows Binary (x86_64) scater_1.38.0.zip (64-bit only)
macOS Binary (x86_64)scater_1.38.0.tgz
macOS Binary (arm64)
Source Repositorygit clone https://git.bioconductor.org/packages/scater
Source Repository (Developer Access)git clone git@git.bioconductor.org:packages/scater
Bioc Package Browserhttps://code.bioconductor.org/browse/scater/
Package Short Urlhttps://bioconductor.org/packages/scater/
Package Downloads ReportDownload Stats
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