clusterExperiment

DOI: 10.18129/B9.bioc.clusterExperiment    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see clusterExperiment.

Compare Clusterings for Single-Cell Sequencing

Bioconductor version: 3.14

Provides functionality for running and comparing many different clusterings of single-cell sequencing data or other large mRNA Expression data sets.

Author: Elizabeth Purdom [aut, cre, cph], Davide Risso [aut]

Maintainer: Elizabeth Purdom <epurdom at stat.berkeley.edu>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("clusterExperiment")

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("clusterExperiment")

 

HTML	R Script	clusterExperiment Vignette
HTML	R Script	Working with Large Datasets
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, RNASeq, Sequencing, SingleCell, Software
Version	2.14.0
In Bioconductor since	BioC 3.4 (R-3.3) (5.5 years)
License	Artistic-2.0
Depends	R (>= 3.6.0), SingleCellExperiment, SummarizedExperiment(>= 1.15.4), BiocGenerics
Imports	methods, NMF, RColorBrewer, ape (>= 5.0), cluster, stats, limma, howmany, locfdr, matrixStats, graphics, parallel, BiocSingular, kernlab, stringr, S4Vectors, grDevices, DelayedArray(>= 0.7.48), HDF5Array(>= 1.7.10), Matrix, Rcpp, edgeR, scales, zinbwave, phylobase, pracma, mbkmeans
LinkingTo	Rcpp
Suggests	BiocStyle, knitr, testthat, MAST, Rtsne, scran, igraph, rmarkdown
SystemRequirements
Enhances
URL
BugReports	https://github.com/epurdom/clusterExperiment/issues
Depends On Me	netSmooth
Imports Me
Suggests Me	netDx, slingshot, tradeSeq
Links To Me
Build Report

Package Archives

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

Source Package	clusterExperiment_2.14.0.tar.gz
Windows Binary	clusterExperiment_2.14.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)
Source Repository	git clone https://git.bioconductor.org/packages/clusterExperiment
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/clusterExperiment
Package Short Url	https://bioconductor.org/packages/clusterExperiment/
Package Downloads Report	Download Stats