This package is for version 3.13 of Bioconductor;
for the stable, up-to-date release version, see
scater.
Single-Cell Analysis Toolkit for Gene Expression Data in R
Bioconductor version: 3.13
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]
Maintainer: Alan O'Callaghan <alan.ocallaghan at outlook.com>
Citation (from within R, enter citation("scater")):
Installation
To install this package, start R (version "4.1") 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
1.20.1
In Bioconductor since
BioC 3.3 (R-3.3) (8 years)
License
GPL-3
Imports
stats, utils, methods, grid, gridExtra, Matrix,
BiocGenerics,
S4Vectors,
SummarizedExperiment,
DelayedArray,
DelayedMatrixStats,
beachmat,
BiocNeighbors,
BiocSingular,
BiocParallel, rlang, ggbeeswarm, viridis, Rtsne, RColorBrewer
System Requirements
See More
Suggests
BiocStyle,
biomaRt, cowplot,
destiny, knitr,
scRNAseq, robustbase, rmarkdown, uwot, NMF, testthat, pheatmap,
snifter,
Biobase
Linking To
Enhances
Imports Me
airpart,
BayesSpace,
CATALYST,
celda,
CelliD,
CellMixS,
ChromSCape,
conclus,
distinct,
IRISFGM,
mia,
miaViz,
muscat,
netDx,
peco,
pipeComp,
scDblFinder,
scPipe,
singleCellTK,
Spaniel,
spatialLIBD,
splatter,
tricycle
Suggests Me
batchelor,
bluster,
CellaRepertorium,
CellTrails,
CiteFuse,
curatedMetagenomicData,
dittoSeq,
DuoClustering2018,
ExperimentSubset,
fcoex,
HCAData,
InteractiveComplexHeatmap,
iSEE,
iSEEu,
M3Drop,
MAST,
mbkmeans,
miloR,
miQC,
monocle,
mumosa,
muscData,
Nebulosa,
SC3,
SCArray,
scds,
schex,
scHOT,
scMerge,
scone,
scp,
scran,
scRepertoire,
simpleSingleCell,
SingleCellMultiModal,
SingleR,
slalom,
snifter,
SummarizedBenchmark,
TabulaMurisData,
tidySingleCellExperiment,
velociraptor,
waddR
Links To Me
Package Archives
Follow Installation instructions to use this package in your R session.
Source Repository
git clone https://git.bioconductor.org/packages/scater
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/scater