SingleCellExperiment

DOI: 10.18129/B9.bioc.SingleCellExperiment    

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

S4 Classes for Single Cell Data

Bioconductor version: 3.7

Defines a S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries.

Author: Aaron Lun [aut, cph], Davide Risso [aut, cre, cph], Keegan Korthauer [ctb]

Maintainer: Davide Risso <risso.davide at gmail.com>

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("SingleCellExperiment")

 

HTML	R Script	An introduction to the SingleCellExperiment class
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, DataRepresentation, Infrastructure, SingleCell, Software
Version	1.2.0
License	GPL-3
Depends	R (>= 3.5), SummarizedExperiment
Imports	S4Vectors, methods, BiocGenerics, utils
LinkingTo
Suggests	testthat, BiocStyle, knitr, rmarkdown, scRNAseq, magrittr, Rtsne
SystemRequirements
Enhances
URL
Depends On Me	BASiCS, clusterExperiment, DropletUtils, iSEE, MAST, scater, scPipe, scran, simpleSingleCell, singleCellTK, splatter, switchde, TENxBrainData, zinbwave
Imports Me	BEARscc, ccfindR, LineagePulse, netSmooth, SC3, scDD, scfind, scmap, SCnorm, slalom
Suggests Me	DEsingle, destiny, phenopath, scFeatureFilter
Links To Me
Build Report

Package Archives

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

Source Package	SingleCellExperiment_1.2.0.tar.gz
Windows Binary	SingleCellExperiment_1.2.0.zip
Mac OS X 10.11 (El Capitan)	SingleCellExperiment_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SingleCellExperiment
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SingleCellExperiment
Package Short Url	http://bioconductor.org/packages/SingleCellExperiment/
Package Downloads Report	Download Stats