APCluster: an R package for affinity propagation clustering

被引：355

作者：

Bodenhofer, Ulrich ^{[1
]}

Kothmeier, Andreas ^{[1
]}

Hochreiter, Sepp ^{[1
]}

机构：

[1] Johannes Kepler Univ Linz, Inst Bioinformat, A-4040 Linz, Austria

来源：

BIOINFORMATICS | 2011年 / 27卷 / 17期

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：

070307 [化学生物学];

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

页码：2463 / 2464

页数：2

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

← 1 2 →