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 (3.21)

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: ), Tuomas Borman [ctb] (ORCID: )

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")

# 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

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	1.35.0
In Bioconductor since	BioC 3.3 (R-3.3) (8.5 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	netSmooth, OSCA.intro, OSCA.workflows, SingleRBook
Imports Me	BayesSpace, CATALYST, CellMixS, CelliD, ChromSCape, FLAMES, M3Drop, MEB, Spaniel, VAExprs, airpart, celda, decontX, distinct, epiregulon.extra, miaViz, mia, peco, pipeComp, scDblFinder, scDotPlot, scMerge, scTreeViz, scviR, singleCellTK, tricycle, spatialLIBD, CAESAR.Suite, PRECAST, SC.MEB
Suggests Me	Banksy, CellTrails, Cepo, CiteFuse, ExperimentSubset, Glimma, InteractiveComplexHeatmap, MAST, MGnifyR, MOSim, MuData, Nebulosa, SC3, SCArray, SPOTlight, SingleCellAlleleExperiment, SingleR, SpatialFeatureExperiment, StabMap, UCell, batchelor, bluster, ccImpute, concordexR, corral, dittoSeq, epiregulon, escheR, ggsc, ggspavis, iSEE, iSEEfier, iSEEhex, iSEEpathways, iSEEtree, iSEEu, mbkmeans, miQC, miloR, monocle, mumosa, raer, scDiagnostics, scHOT, scPipe, scRepertoire, scds, schex, scone, scp, scran, sketchR, slalom, smartid, smoothclust, spatialHeatmap, speckle, splatter, standR, tidySingleCellExperiment, tidySpatialExperiment, velociraptor, 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_1.35.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
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