APCluster: an R package for affinity propagation clustering

被引:333
作者
Bodenhofer, Ulrich [1 ]
Kothmeier, Andreas [1 ]
Hochreiter, Sepp [1 ]
机构
[1] Johannes Kepler Univ Linz, Inst Bioinformat, A-4040 Linz, Austria
关键词
NETWORKS;
D O I
10.1093/bioinformatics/btr406
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
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.
引用
收藏
页码:2463 / 2464
页数:2
相关论文
共 14 条
[1]   Clustering by passing messages between data points [J].
Frey, Brendan J. ;
Dueck, Delbert .
SCIENCE, 2007, 315 (5814) :972-976
[2]   Temporal clustering by affinity propagation reveals transcriptional modules in Arabidopsis thaliana [J].
Kiddle, Steven J. ;
Windram, Oliver P. F. ;
McHattie, Stuart ;
Mead, Andrew ;
Beynon, Jim ;
Buchanan-Wollaston, Vicky ;
Denby, Katherine J. ;
Mukherjee, Sach .
BIOINFORMATICS, 2010, 26 (03) :355-362
[3]   Clustering by soft-constraint affinity propagation: applications to gene-expression data [J].
Leone, Michele ;
Sumedha ;
Weigt, Martin .
BIOINFORMATICS, 2007, 23 (20) :2708-2715
[4]   Detecting microarray data supported microRNA-mRNA interactions [J].
Liu, Hui ;
Zhou, Shuigeng ;
Guan, Jihong .
INTERNATIONAL JOURNAL OF DATA MINING AND BIOINFORMATICS, 2010, 4 (06) :639-655
[5]   Complex Networks Govern Coiled-Coil Oligomerization - Predicting and Profiling by Means of a Machine Learning Approach [J].
Mahrenholz, Carsten C. ;
Abfalter, Ingrid G. ;
Bodenhofer, Ulrich ;
Volkmer, Rudolf ;
Hochreiter, Sepp .
MOLECULAR & CELLULAR PROTEOMICS, 2011, 10 (05)
[6]   Coiled coil domains: Stability, specificity, and biological implications [J].
Mason, JM ;
Arndt, KM .
CHEMBIOCHEM, 2004, 5 (02) :170-176
[7]   A New Clustering of Antibody CDR Loop Conformations [J].
North, Benjamin ;
Lehmann, Andreas ;
Dunbrack, Roland L., Jr. .
JOURNAL OF MOLECULAR BIOLOGY, 2011, 406 (02) :228-256
[8]   TASSER_low-zsc: An approach to improve structure prediction using low z-score-ranked templates [J].
Pandit, Shashi B. ;
Skolnick, Jeffrey .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2010, 78 (13) :2769-2780
[9]   Arena3D: visualization of biological networks in 3D [J].
Pavlopoulos, Georgios A. ;
O'Donoghue, Sean I. ;
Satagopam, Venkata P. ;
Soldatos, Theodoros G. ;
Pafilis, Evangelos ;
Schneider, Reinhard .
BMC SYSTEMS BIOLOGY, 2008, 2
[10]   A Poisson-based adaptive affinity propagation clustering for SAGE data [J].
Tang, DongMing ;
Zhu, QingXin ;
Yang, Fan .
COMPUTATIONAL BIOLOGY AND CHEMISTRY, 2010, 34 (01) :63-70