To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("scater")

In most cases, you don't need to download the package archive at all.

scater

DOI: 10.18129/B9.bioc.scater    

This is the development version of scater; for the stable release version, see scater.

Single-cell analysis toolkit for gene expression data in R

Bioconductor version: Development (3.6)

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

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("scater")

Documentation

HTML R Script An introduction to the scater package
HTML R Script An introduction to the scater package
HTML R Script Data visualisation methods in scater
HTML R Script Quality control with scater
HTML R Script Transition from SCESet to SingleCellExperiment
PDF   Reference Manual
Text   NEWS

Details

biocViews Coverage, DataImport, DataRepresentation, DimensionReduction, GeneExpression, Infrastructure, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.5.19
In Bioconductor since BioC 3.3 (R-3.3) (1.5 years)
License GPL (>= 2)
Depends R (>= 3.4), Biobase, ggplot2, SingleCellExperiment, SummarizedExperiment
Imports biomaRt, BiocGenerics, data.table, dplyr, edgeR, ggbeeswarm, grid, limma, Matrix, matrixStats, methods, parallel, plyr, reshape2, rhdf5, rjson, S4Vectors, shiny, shinydashboard, stats, tximport, utils, viridis, Rcpp
LinkingTo Rhdf5lib, Rcpp, beachmat
Suggests BiocStyle, beachmat, cowplot, cluster, destiny, knitr, monocle, mvoutlier, rmarkdown, Rtsne, testthat, magrittr
SystemRequirements C++11
Enhances
URL http://bioconductor.org/packages/scater/
BugReports https://support.bioconductor.org/
Depends On Me splatter
Imports Me scran
Suggests Me phenopath, SC3, switchde
Build Report  

Package Archives

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

Source Package scater_1.5.19.tar.gz
Windows Binary scater_1.5.19.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) scater_1.5.19.tgz
Source Repository git clone https://git.bioconductor.org/packages/scater
Package Short Url http://bioconductor.org/packages/scater/
Package Downloads Report Download Stats

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