scater

Single-Cell Analysis Toolkit for Gene Expression Data in R

Bioconductor version: 3.24 · Package version: 1.41.2

A collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control and visualization.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("scater")

Maintainer	Alan O'Callaghan <alan.ocallaghan@outlook.com>
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: <https://orcid.org/0000-0001-5537-637X>), Tuomas Borman [ctb] (ORCID: <https://orcid.org/0000-0002-8563-8884>)
License	GPL-3
URL	http://bioconductor.org/packages/scater/
Bug Reports	https://support.bioconductor.org/
Downloads rank	11044
Source branch	devel
biocViews	Coverage, DataImport, DataRepresentation, DimensionReduction, GeneExpression, ImmunoOncology, Infrastructure, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization

Follow the installation instructions to use this package in your R session.

Dependencies

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

Suggests: BiocStyle, DelayedMatrixStats, snifter, densvis, cowplot, biomaRt, knitr, scRNAseq, robustbase, rmarkdown, testthat, Biobase, scattermore, ggrastr, MASS

Reverse dependencies

Depends On Me (3): chevreulProcess, netSmooth, omicsGMF

Imports Me (35): airpart, augere.solo, BayesSpace, blase, CAESAR.Suite, CATALYST, CellMixS, chevreulPlot, ChromSCape, clustSIGNAL, distinct, DoReMiTra, epiregulon.extra, FLAMES, M3Drop, MEB, mia, miaDash, miaViz, muscat, peco, pipeComp, PRECAST, RegionalST, scDblFinder, scDotPlot, scMerge, scTreeViz, shinyDSP, singleCellTK, SpaceTrooper, Spaniel, spatialLIBD, tricycle, VAExprs