scater

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see scater.

Single-Cell Analysis Toolkit for Gene Expression Data in R

Bioconductor version: 3.21

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, enter citation("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 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

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 1.36.0

In Bioconductor since BioC 3.3 (R-3.3) (9.5 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, ggrastr

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

Linking To

Enhances

Depends On Me chevreulProcess, netSmooth, OSCA.advanced, OSCA.basic, OSCA.intro, OSCA.multisample, OSCA.workflows, SingleRBook

Imports Me airpart, BayesSpace, 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, Spaniel, tricycle, VAExprs, spatialLIBD, PRECAST

Suggests Me alabaster.sfe, APL, Banksy, batchelor, bluster, ccImpute, CellTrails, Cepo, CiteFuse, concordexR, corral, crumblr, dandelionR, dittoSeq, dreamlet, epiregulon, escheR, ExperimentSubset, ggsc, ggspavis, Glimma, HoloFoodR, InteractiveComplexHeatmap, iSEE, iSEEfier, iSEEhex, iSEEpathways, iSEEtree, iSEEu, jazzPanda, MAST, mbkmeans, MGnifyR, miloR, miQC, monocle, MOSim, MuData, mumosa, Nebulosa, raer, ReactomeGSA, SC3, SCArray, scDiagnostics, scds, schex, scHOT, scone, scp, scPipe, scran, scRepertoire, SingleCellAlleleExperiment, sketchR, slalom, smartid, smoothclust, SpatialFeatureExperiment, spatialHeatmap, speckle, splatter, SPOTlight, StabMap, standR, SVP, tidySingleCellExperiment, tidySpatialExperiment, UCell, velociraptor, Voyager, waddR, curatedMetagenomicData, DuoClustering2018, HCAData, HCATonsilData, MerfishData, MouseAgingData, muscData, SingleCellMultiModal, TabulaMurisData, tuberculosis, simpleSingleCell, spicyWorkflow, Canek, ProFAST, SCdeconR, scellpam, SuperCell

Links To Me

Build Report Build Report

Package Archives

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

Source Package scater_1.36.0.tar.gz

Windows Binary (x86_64) scater_1.36.0.zip

macOS Binary (x86_64) scater_1.36.0.tgz

macOS Binary (arm64) scater_1.35.0.tgz

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