DOI: 10.18129/B9.bioc.clusterExperiment    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see clusterExperiment.

Compare Clusterings for Single-Cell Sequencing

Bioconductor version: 3.13

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 "4.1") and enter:

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


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


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


biocViews Clustering, RNASeq, Sequencing, SingleCell, Software
Version 2.12.0
In Bioconductor since BioC 3.4 (R-3.3) (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
Depends On Me netSmooth
Imports Me netDx
Suggests Me slingshot, tradeSeq
Links To Me
Build Report  

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Source Package clusterExperiment_2.12.0.tar.gz
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macOS 10.13 (High Sierra) clusterExperiment_2.11.3.tgz
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