scater

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see scater.

Single-Cell Analysis Toolkit for Gene Expression Data in R


Bioconductor version: 3.9

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, cre], Kieran Campbell [aut], Aaron Lun [aut, ctb], Quin Wills [aut], Vladimir Kiselev [ctb]

Maintainer: Davis McCarthy <davis at ebi.ac.uk>

Citation (from within R, enter citation("scater")):

Installation

To install this package, start R (version "3.6") 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")
1. An introduction to the scater package HTML R Script
2. Data visualisation methods in scater HTML R Script
3. Quality control with scater HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Coverage, DataImport, DataRepresentation, DimensionReduction, GeneExpression, ImmunoOncology, Infrastructure, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.12.2
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License GPL-3
Depends R (>= 3.6), SingleCellExperiment, ggplot2
Imports BiocGenerics, SummarizedExperiment, Matrix, dplyr, ggbeeswarm, grid, DelayedArray, DelayedMatrixStats, methods, S4Vectors, stats, utils, viridis, Rcpp, BiocNeighbors, BiocSingular, BiocParallel
System Requirements C++11
URL http://bioconductor.org/packages/scater/
Bug Reports https://support.bioconductor.org/
See More
Suggests BiocStyle, biomaRt, beachmat, cowplot, destiny, knitr, mvoutlier, rmarkdown, Rtsne, uwot, testthat, magrittr, pheatmap, Biobase, limma
Linking To Rcpp, beachmat
Enhances
Depends On Me netSmooth
Imports Me batchelor, CATALYST, CellMixS, scran, splatter
Suggests Me CellTrails, DuoClustering2018, HCAData, iSEE, M3Drop, MAST, mbkmeans, monocle, SC3, scds, scMerge, simpleSingleCell, slalom, SummarizedBenchmark, TabulaMurisData
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package scater_1.12.2.tar.gz
Windows Binary scater_1.12.2.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) scater_1.12.2.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 3.9 Source Archive