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("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 | ||
| 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 |