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

 

   

Single-cell analysis toolkit for gene expression data in R

Bioconductor version: Release (3.5)

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

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
PDF   Reference Manual
Text   NEWS

Details

biocViews DataImport, DataRepresentation, DimensionReduction, GeneExpression, Infrastructure, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.4.0
In Bioconductor since BioC 3.3 (R-3.3) (1 year)
License GPL (>= 2)
Depends R (>= 3.3), Biobase, ggplot2, methods
Imports biomaRt, BiocGenerics, data.table, dplyr, edgeR, ggbeeswarm, grid, limma, Matrix, matrixStats, parallel, plyr, reshape2, rhdf5, rjson, shiny, shinydashboard, stats, tximport, utils, viridis
LinkingTo
Suggests BiocStyle, cowplot, cluster, destiny, knitr, monocle, mvoutlier, rmarkdown, Rtsne, testthat, magrittr
SystemRequirements
Enhances
URL http://bioconductor.org/packages/scater/
BugReports https://support.bioconductor.org/
Depends On Me scran, splatter
Imports Me Glimma, SC3
Suggests Me switchde
Build Report  

Package Archives

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

Package Source scater_1.4.0.tar.gz
Windows Binary scater_1.3.35.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) scater_1.4.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/scater/tree/release-3.5
Package Short Url http://bioconductor.org/packages/scater/
Package Downloads Report Download Stats

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