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 outlook.com>
citation("scater")):
Installation
To install this package, start R (version "4.3") 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")| Overview of scater functionality | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| 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 |
| Linking To | |
| Suggests | BiocStyle, snifter, cowplot, biomaRt, knitr, scRNAseq, robustbase, rmarkdown, testthat, Biobase, scattermore |
| System Requirements | |
| Enhances | |
| URL | http://bioconductor.org/packages/scater/ |
| Bug Reports | https://support.bioconductor.org/ |
See More
| 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 |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scater_1.28.0.tar.gz |
| Windows Binary | scater_1.28.0.zip |
| macOS Binary (x86_64) | scater_1.28.0.tgz |
| 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 |