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Compare Clusterings for Single-Cell Sequencing

Bioconductor version: Release (3.18)

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>

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


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews Clustering, RNASeq, Sequencing, SingleCell, Software
Version 2.22.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 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
System Requirements
Bug Reports https://github.com/epurdom/clusterExperiment/issues
See More
Suggests BiocStyle, knitr, testthat, MAST, Rtsne, scran, igraph, rmarkdown
Linking To Rcpp
Depends On Me netSmooth
Imports Me
Suggests Me netDx, slingshot, tradeSeq
Links To Me
Build Report Build Report

Package Archives

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

Source Package clusterExperiment_2.22.0.tar.gz
Windows Binary clusterExperiment_2.22.0.zip
macOS Binary (x86_64) clusterExperiment_2.22.0.tgz
macOS Binary (arm64) clusterExperiment_2.22.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/clusterExperiment
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/clusterExperiment
Bioc Package Browser https://code.bioconductor.org/browse/clusterExperiment/
Package Short Url https://bioconductor.org/packages/clusterExperiment/
Package Downloads Report Download Stats