scater
Single-Cell Analysis Toolkit for Gene Expression Data in R
Bioconductor version: 3.23 · Package version: 1.40.2
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")Details
| 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 | 10351 |
| Source branch | RELEASE_3_23 |
| biocViews | Coverage, DataImport, DataRepresentation, DimensionReduction, GeneExpression, ImmunoOncology, Infrastructure, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization |
Documentation
Download
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 (38): airpart, BayesSpace, blase, CAESAR.Suite, CATALYST, celda, CelliD, CellMixS, chevreulPlot, ChromSCape, clustSIGNAL, decontX, distinct, DoReMiTra, epiregulon.extra, FLAMES, M3Drop, MEB, mia, miaDash, miaViz, muscat, peco, pipeComp, PRECAST, RegionalST, scDblFinder, scDotPlot, scMerge, scTreeViz, scviR, shinyDSP, singleCellTK, SpaceTrooper, Spaniel, spatialLIBD, tricycle, VAExprs
Suggests Me (111): alabaster.sfe, anglemania, APL, Banksy, BatChef, batchelor, bluster, Canek, ccImpute, CellMentor, CellTrails, Cepo, CiteFuse, coFAST, concordexR, Coralysis, corral, crumblr, curatedMetagenomicData, dandelionR, DeeDeeExperiment, dittoSeq, DOtools, dreamlet, DuoClustering2018, epiregulon, escheR, ExperimentSubset, futurize, ggsc, ggspavis, Glimma, GSABenchmark, hammers, HCAData, HCATonsilData, HoloFoodR, HVP, Ibex, immLynx, InteractiveComplexHeatmap, iSEE, iSEEfier, iSEEhex, iSEEpathways, iSEEtree, iSEEu, jazzPanda, MAST, mbkmeans, MerfishData, MGnifyR, miaTime, miloR, miQC, monocle, MOSim, MouseAgingData, msqrob2, MuData, mumosa, muscData, Nebulosa, ProFAST, raer, ReactomeGSA, SanityR, SC3, SCArray, scDiagnostics, scds, scellpam, scGraphVerse, schex, scHOT, scLANE, scLang, scone, scp, scPipe, scran, scrapper, scRepertoire, Seqtometry, simPIC, simpleSingleCell, SingleCellAlleleExperiment, SingleCellMultiModal, sketchR, slalom, smartid, smoothclust, SpaNorm, SpatialFeatureExperiment, spatialHeatmap, speckle, splatter, SPOTlight, StabMap, standR, SuperCell, SuperCellCyto, SVP, TabulaMurisData, tidySingleCellExperiment, tidySpatialExperiment, tuberculosis, UCell, velociraptor, Voyager, waddR