SingleCellExperiment

DOI: 10.18129/B9.bioc.SingleCellExperiment    

S4 Classes for Single Cell Data

Bioconductor version: Release (3.8)

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 (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("SingleCellExperiment", version = "3.8")

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")

 

HTML R Script 1. An introduction to the SingleCellExperiment class
HTML R Script 2. Developing around the SingleCellExperiment class
PDF   Reference Manual
Text   NEWS

Details

biocViews DataImport, DataRepresentation, Infrastructure, SingleCell, Software
Version 1.4.0
License GPL-3
Depends R (>= 3.5), SummarizedExperiment
Imports S4Vectors, methods, BiocGenerics, utils, stats
LinkingTo
Suggests testthat, BiocStyle, knitr, rmarkdown, scRNAseq, magrittr, Rtsne
SystemRequirements
Enhances
URL
Depends On Me allenpvc, BASiCS, CellTrails, clusterExperiment, cydar, DropletUtils, iSEE, LoomExperiment, MAST, scater, scPipe, scran, simpleSingleCell, singleCellTK, splatter, switchde, TENxBrainData, TENxPBMCData, zinbwave
Imports Me bayNorm, BEARscc, ccfindR, CoGAPS, LineagePulse, netSmooth, SC3, scDD, scfind, scmap, SCnorm, scruff, slalom, slingshot
Suggests Me DEsingle, destiny, DuoClustering2018, FCBF, phenopath, scFeatureFilter, TabulaMurisData
Links To Me
Build Report  

Package Archives

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

Source Package SingleCellExperiment_1.4.0.tar.gz
Windows Binary SingleCellExperiment_1.4.0.zip
Mac OS X 10.11 (El Capitan) SingleCellExperiment_1.4.0.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

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