R package of techniques for comparing clusterings of single-cell sequencing data
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R package: clusterExperiment

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

News and Updates

  • Note that some important bugs were fixed since the Bioconductor release. They have been updated in the release version of Bioconductor (version 2.0.2) as well as the development version.

  • Version 2.0.0 is now available on Bioconductor with many new changes. Checkout out a brief description of the major changes. For complete details, see the NEWS file.

    The new 2.0.0 version does make use of packages only available in the new release of bioconductor (and thus the new release of R).


Installation instructions

Installation From Bioconductor

We recommend installation of the package via bioconductor.


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).

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 https://github.com/epurdom/clusterExperiment/issues to submit issues, bug reports, and comments.