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>

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

Installation

To install this package, start R (version "3.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SingleCellExperiment")

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

Details

biocViews DataImport, DataRepresentation, Infrastructure, SingleCell, Software
Version 1.2.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL-3
Depends R (>= 3.5), SummarizedExperiment
Imports S4Vectors, methods, BiocGenerics, utils
System Requirements
URL
See More
Suggests testthat, BiocStyle, knitr, rmarkdown, scRNAseq, magrittr, Rtsne
Linking To
Enhances
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 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 https://bioconductor.org/packages/SingleCellExperiment/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive