scater

DOI: 10.18129/B9.bioc.scater    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see scater.

Single-Cell Analysis Toolkit for Gene Expression Data in R

Bioconductor version: 3.7

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>

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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scater")

 

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

Details

biocViews	Coverage, DataImport, DataRepresentation, DimensionReduction, GeneExpression, Infrastructure, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version	1.8.4
In Bioconductor since	BioC 3.3 (R-3.3) (2.5 years)
License	GPL (>= 2)
Depends	R (>= 3.5), Biobase, ggplot2, SingleCellExperiment, SummarizedExperiment
Imports	BiocGenerics, data.table, dplyr, edgeR, ggbeeswarm, grid, limma, Matrix, DelayedMatrixStats, methods, parallel, plyr, reshape2, rhdf5, rjson, S4Vectors, shiny, shinydashboard, stats, tximport, utils, viridis, Rcpp (>= 0.12.14), DelayedArray
LinkingTo	Rhdf5lib, Rcpp, beachmat
Suggests	BiocStyle, biomaRt, beachmat, cowplot, cluster, destiny, knitr, monocle, mvoutlier, rmarkdown, Rtsne, testthat, magrittr, pheatmap, DropletUtils, irlba
SystemRequirements	C++11
Enhances
URL	http://bioconductor.org/packages/scater/
BugReports	https://support.bioconductor.org/
Depends On Me	netSmooth, simpleSingleCell
Imports Me	scran, splatter
Suggests Me	iSEE, monocle, SC3, slalom, SummarizedBenchmark
Links To Me
Build Report

Package Archives

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

Source Package	scater_1.8.4.tar.gz
Windows Binary	scater_1.8.4.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	scater_1.8.4.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scater
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scater
Package Short Url	http://bioconductor.org/packages/scater/
Package Downloads Report	Download Stats