SingleCellExperiment

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see SingleCellExperiment.

S4 Classes for Single Cell Data

DOI: 10.18129/B9.bioc.SingleCellExperiment

Bioconductor version: 3.6

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]

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

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

Installation

To install this package, start R (version "3.4") 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

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, DataRepresentation, Infrastructure, SingleCell, Software

Version 1.0.0

In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)

License GPL-3

Depends R (>= 3.4), SummarizedExperiment

Imports S4Vectors, methods, BiocGenerics, utils

System Requirements

URL

Suggests testthat, BiocStyle, knitr, scRNAseq, magrittr, Rtsne

Linking To

Enhances

Depends On Me BASiCS, scater, scPipe, scran, splatter, switchde, zinbwave

Imports Me SC3, scDD, scfind, scmap, slalom

Suggests Me phenopath

Links To Me

Build Report Build Report

Package Archives

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

Source Package SingleCellExperiment_1.0.0.tar.gz

Windows Binary SingleCellExperiment_1.0.0.zip

Mac OS X 10.11 (El Capitan) SingleCellExperiment_1.0.0.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/

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Old Source Packages for BioC 3.6 Source Archive