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Bioinformatics

APCluster - An R Package for Affinity Propagation Clustering

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 (cf. Affinity Propagation Website) 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.

The current version of the package is 1.4.8 (released 2019-08-21).

Getting started

  1. To load the package, enter "library(apcluster)" in your R session.
  2. To view the user manual, enter "vignette("apcluster")".
  3. To do a first example, enter "example(apcluster)".

Documentation

  1. User Manual: PDF
  2. Reference Manual: PDF

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).
  1. Complete recording of webinar: YouTube Video (length: 59:17)
  2. Slides of webinar: PDF (6.6MB)
  3. R code used in webinar: R code (4KB)

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 consider posting to the R-help Mailing List or on StackOverflow. For other matters regarding the package, please contact apcluster@bioinf.jku.at.

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.