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scater

This is the development version of scater; for the stable release version, see scater.

Single-Cell Analysis Toolkit for Gene Expression Data in R


Bioconductor version: Development (3.20)

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] , Tuomas Borman [ctb]

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

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

Installation

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


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Overview of scater functionality HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Coverage, DataImport, DataRepresentation, DimensionReduction, GeneExpression, ImmunoOncology, Infrastructure, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.33.4
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, MatrixGenerics, SparseArray, DelayedArray, 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/
See More
Suggests BiocStyle, DelayedMatrixStats, snifter, densvis, cowplot, biomaRt, knitr, scRNAseq, robustbase, rmarkdown, testthat, Biobase, scattermore
Linking To
Enhances
Depends On Me netSmooth, OSCA.advanced, OSCA.basic, OSCA.intro, OSCA.multisample, OSCA.workflows
Imports Me airpart, BayesSpace, CATALYST, celda, CelliD, CellMixS, ChromSCape, decontX, distinct, epiregulon.extra, FLAMES, M3Drop, MEB, mia, miaViz, muscat, peco, pipeComp, RegionalST, scDblFinder, scDotPlot, 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, Canek, ProFAST, SCdeconR, scellpam
Links To Me
Build Report Build Report

Package Archives

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

Source Package scater_1.33.4.tar.gz
Windows Binary scater_1.33.3.zip
macOS Binary (x86_64) scater_1.33.4.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