APCluster - An R Package for Affinity Propagation Clustering
This is a legacy page. The package is now hosted on GitHub.
In order to make Affinity Propagation Clustering [Frey & Dueck, 2007] accessible to a wider audience in bioinformatics, we ported the Matlab code published by the authors Frey and Dueck to R.Installation
The package is available through CRAN - The Comprehensive R Archive Network (click here to view the archive entry of the package). Therefore, the simplest way to install the package is to enter
install.packages("apcluster")
into your R session. If, for what reason ever, you prefer to install the package manually, follow the instructions in the user manual.
User support
If you encounter any issues or if you have any question that might be of interest also for other users, before writing a private message to the package developers/maintainers, please create an issue in the source code repository and also consider posting on to the R-help Mailing List or on StackOverflow.Webinar "Introduction to apcluster"
On June 13, 2013, the maintainer of the package, Ulrich Bodenhofer, gave a webinar on the apcluster package. The webinar was hosted by the Orange County R User Group and moderated by its president, Ray DiGiacomo, Jr. The demo uses Version 1.3.2 of the package (released June 11, 2013).- Complete recording of webinar: YouTube Video (length: 59:17)
- Slides of webinar: PDF (6.6MB)
- R code used in webinar: R code (4KB)
Citing this package
If you use this package for research that is published later, you are kindly asked to cite it as follows:U. Bodenhofer, A. Kothmeier, and S. Hochreiter (2011). APCluster: an R package for affinity propagation clustering. Bioinformatics 27:2463-2464. DOI: 10.1093/bioinformatics/btr406.
Moreover, we insist that, any time you use/cite the package, you also cite the original paper in which affinity propagation has been introduced:B. J. Frey and D. Dueck (2007). Clustering by passing messages between data points. Science, 315:972-976. DOI: 10.1126/science.1136800.