R package: clusterExperiment

Functions for running and comparing many different clusterings of single-cell sequencing data.

News and Updates


Installation instructions

Installation From Bioconductor

We recommend installation of the package via bioconductor.

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

To install the most recent version of the package available on the development branch of bioconductor, follow the above instructions, after downloading the development version of bioconductor (see here for instructions).

If you are having problems installing/updating the package gsl from source because your gsl installation is not found, this answer (and the comment following it) on stackoverflow may be of help.

Installation of Github Version:

We generally try to keep the bioconductor devel version up-to-date with the master branch of this git repository. But since this can require installing R and/or bioconductor development version, it can be convenient to be able to get just the most recent version from github.

You can install the github version via


Development branch:

The develop branch is our development branch where we are actively updating features, and may contain bugs or be in the process of being updated. You should not use the develop branch unless it passes TravisCI checks (see below) and you want to be using a very beta version.

The development branch can be installed via the install_github command above, but indicating the develop branch:

install_github("epurdom/clusterExperiment", ref="develop")

Status Checks

Below are status checks for the package. Note that occassionally errors do not appear here immediately. Clicking on the link will give you the most up-to-date status.

| Resource: | Status | | ------------- | ------------ | | Bioc Release | BiocDevel Status| | Bioc Development | BiocDevel Status| | Travis CI master | Build Status | | Travis CI develop | Build Status | | Appveyor master | AppVeyor Build Status | | Appveyor develop | AppVeyor Build Status |

Issues and bug reports

Please use to submit issues, bug reports, and comments.

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clusterExperiment documentation built on Feb. 11, 2021, 2 a.m.