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.
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).
The paper acompanying this package can be found at:
Davide Risso, Liam Purvis, Russell Fletcher, Diya Das, John Ngai, Sandrine Dudoit, and Elizabeth Purdom (March 2018) "clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets" bioRxiv, (https://www.biorxiv.org/content/early/2018/03/12/280545)[https://www.biorxiv.org/content/early/2018/03/12/280545].
There is a github repository ((epurdom/RSECPaper)[https://github.com/epurdom/RSECPaper] for this paper that gives the code for reproducing the analysis in that manuscript.
A (F1000 workflow)[https://f1000research.com/articles/6-1158/v1] demonstrating the use of RSEC for clustering as part of trajectory estimation with the package
slingshotand normalization with
Perraudeau F, Risso D, Street K, Purdom E, and Dudoit S (2017) "Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference" F1000Research 6:1158.
A compiled version of the vignette (i.e. tutorial) of the github version of
clusterExperiment(corresponding to the
masterbranch) can be found (here)[http://bioconductor.org/packages/devel/bioc/vignettes/clusterExperiment/inst/doc/clusterExperimentTutorial.html]
The compiled version of the version of
clusterExperimentavailable with the latest release of Bioconductor can be found (here)[http://bioconductor.org/packages/release/bioc/vignettes/clusterExperiment/inst/doc/clusterExperimentTutorial.html]
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
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
library(devtools) install_github("epurdom/clusterExperiment", ref="develop")
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.
|Travis CI master|
|Travis CI develop|
Issues and bug reports
Please use https://github.com/epurdom/clusterExperiment/issues to submit issues, bug reports, and comments.