DOI: 10.18129/B9.bioc.scater  

Single-Cell Analysis Toolkit for Gene Expression Data in R

Bioconductor version: Release (3.17)

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]

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

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


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biocViews Coverage, DataImport, DataRepresentation, DimensionReduction, GeneExpression, ImmunoOncology, Infrastructure, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.28.0
In Bioconductor since BioC 3.3 (R-3.3) (7.5 years)
License GPL-3
Depends SingleCellExperiment, scuttle, ggplot2
Imports stats, utils, methods, Matrix, BiocGenerics, S4Vectors, SummarizedExperiment, DelayedArray, DelayedMatrixStats, beachmat, BiocNeighbors, BiocSingular, BiocParallel, rlang, ggbeeswarm, viridis, Rtsne, RColorBrewer, RcppML, uwot, pheatmap, ggrepel, densvis, ggrastr
Suggests BiocStyle, snifter, cowplot, biomaRt, knitr, scRNAseq, robustbase, rmarkdown, testthat, Biobase, scattermore
Depends On Me netSmooth
Imports Me airpart, BayesSpace, CATALYST, celda, CelliD, CellMixS, ChromSCape, distinct, FLAMES, IRISFGM, MEB, mia, miaViz, muscat, peco, pipeComp, scDblFinder, scMerge, scTreeViz, scviR, singleCellTK, Spaniel, spatialHeatmap, spatialLIBD, tricycle, VAExprs
Suggests Me APL, batchelor, bluster, ccImpute, CellaRepertorium, CellTrails, Cepo, CiteFuse, concordexR, corral, curatedMetagenomicData, dittoSeq, DuoClustering2018, ExperimentSubset, fcoex, ggspavis, Glimma, HCAData, InteractiveComplexHeatmap, iSEE, iSEEhex, iSEEu, M3Drop, MAST, mbkmeans, miloR, miQC, monocle, MuData, mumosa, muscData, Nebulosa, netDx, SC3, SCArray, scds, schex, scHOT, scone, scp, scPipe, scran, scRepertoire, simpleSingleCell, SingleCellMultiModal, SingleR, slalom, speckle, spicyWorkflow, splatter, SPOTlight, standR, SummarizedBenchmark, TabulaMurisData, tidySingleCellExperiment, traviz, tuberculosis, UCell, velociraptor, Voyager, waddR
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Source Package scater_1.28.0.tar.gz
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