DOI: 10.18129/B9.bioc.clusterExperiment    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see clusterExperiment.

Compare Clusterings for Single-Cell Sequencing

Bioconductor version: 3.8

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], Marla Johnson [ctb]

Maintainer: Elizabeth Purdom <epurdom at>

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


To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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:



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biocViews Clustering, RNASeq, Sequencing, SingleCell, Software
Version 2.2.0
In Bioconductor since BioC 3.4 (R-3.3) (2.5 years)
License Artistic-2.0
Depends R (>= 3.5.0), SingleCellExperiment, SummarizedExperiment, BiocGenerics
Imports methods, NMF, RColorBrewer, ape (>= 5.0), phylobase, cluster, stats, limma, dendextend, howmany, locfdr, matrixStats, graphics, parallel, RSpectra, kernlab, stringr, S4Vectors, grDevices, Rcpp, HDF5Array(>= 1.7.10), DelayedArray(>= 0.5.31), edgeR, scales, zinbwave
LinkingTo Rcpp
Suggests BiocStyle, knitr, testthat, scRNAseq, MAST, Rtsne, scran, igraph
Depends On Me netSmooth
Imports Me slingshot
Suggests Me
Links To Me
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Source Package clusterExperiment_2.2.0.tar.gz
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Mac OS X 10.11 (El Capitan) clusterExperiment_2.2.0.tgz
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