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APCluster: an R package for affinity propagation clustering
Abstract
Summary: Affinity propagation (AP) clustering has recently gained increasing popularity in bioinformatics. AP clustering has the advantage that it allows for determining typical cluster members, the so-called exemplars. We provide an R implementation of this promising new clustering technique to account for the ubiquity of R in bioinformatics. This article introduces the package and presents an application from structural biology. Availability: The R package apcluster is available via CRAN—The Comprehensive R Archive Network: http://cran.r-project.org/web/packages/apcluster Contact: apcluster@bioinf.jku.at; bodenhofer@bioinf.jku.at
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Cites
A new clustering of antibody CDR loop conformations
North, B., Lehmann, A., & Dunbrack, R. L. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.10.030 · Cited by 380
Mahrenholz, C. C., Abfalter, I. G., Bodenhofer, U., Volkmer, R., & Hochreiter, S. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.004994 · Cited by 47
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Cited by
Saltz, J., Gupta, R., Hou, L., Kurc, T., Singh, P., Nguyen, V., Samaras, D., Shroyer, K. R., Zhao, T., Batiste, R., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.03.086 · Cited by 1,027
Biological interpretation of genome-wide association studies using predicted gene functions
Pers, T. H., Karjalainen, J. M., Chan, Y., Westra, H.-J., Wood, A. R., Yang, J., Lui, J. C., Vedantam, S., Gustafsson, S., Esko, T., et al. (2015) · Nature Communications · doi:10.1038/ncomms6890 · Cited by 787
Ligthart, S., Vaez, A., Võsa, U., Stathopoulou, M. G., de Vries, P. S., Prins, B. P., Van der Most, P. J., Tanaka, T., Naderi, E., Rose, L. M., et al. (2018) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2018.09.009 · Cited by 419
Identification of context-dependent expression quantitative trait loci in whole blood
Zhernakova, D. V., Deelen, P., Vermaat, M., van Iterson, M., van Galen, M., Arindrarto, W., van 't Hof, P., Mei, H., van Dijk, F., Westra, H.-J., et al. (2017) · Nature Genetics · doi:10.1038/ng.3737 · Cited by 416
Costa, M., Manton, J. D., Ostrovsky, A. D., Prohaska, S., & Jefferis, G. S. X. E. (2016) · Neuron · doi:10.1016/j.neuron.2016.06.012 · Cited by 294
Metadata
- Authors
- Bodenhofer, U., Kothmeier, A., & Hochreiter, S.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-07-06
- Volume
- 27
- Issue
- 17
- Pages
- 2463-2464
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2137799805
- Cited by
- 479
- References
- 2
- FWCI
- 10.64
- Type
- journal article
- Language
- en
- Open access
- closed
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