scater
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("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")| 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 | 1.20.1 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8 years) |
| License | GPL-3 |
| Depends | SingleCellExperiment, scuttle, ggplot2 |
| Imports | stats, utils, methods, grid, gridExtra, Matrix, BiocGenerics, S4Vectors, SummarizedExperiment, DelayedArray, DelayedMatrixStats, beachmat, BiocNeighbors, BiocSingular, BiocParallel, rlang, ggbeeswarm, viridis, Rtsne, RColorBrewer |
| System Requirements | |
| URL | http://bioconductor.org/packages/scater/ |
| Bug Reports | https://support.bioconductor.org/ |
See More
| Suggests | BiocStyle, biomaRt, cowplot, destiny, knitr, scRNAseq, robustbase, rmarkdown, uwot, NMF, testthat, pheatmap, snifter, Biobase |
| Linking To | |
| Enhances | |
| Depends On Me | netSmooth |
| 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 | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scater_1.20.1.tar.gz |
| Windows Binary | scater_1.20.1.zip |
| macOS 10.13 (High Sierra) | scater_1.20.1.tgz |
| 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 |
| Old Source Packages for BioC 3.13 | Source Archive |