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Bioconductor - scater

scater

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

Single-Cell Analysis Toolkit for Gene Expression Data in R

Bioconductor version: Release (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: 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")): 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")

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 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 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.

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