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Compare Clusterings for Single-Cell Sequencing

Bioconductor version: Release (3.19)

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>

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


To install this package, start R (version "4.4") 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 2.24.0
In Bioconductor since BioC 3.4 (R-3.3) (8 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, 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
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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
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Package Archives

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

Source Package clusterExperiment_2.24.0.tar.gz
Windows Binary
macOS Binary (x86_64) clusterExperiment_2.24.0.tgz
macOS Binary (arm64) clusterExperiment_2.24.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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