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Bioinformatics Advance Access published online on July 2, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn307
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

ChemmineR: A Compound Mining Framework for R

Yiqun Cao 1, Anna Charisi 2, Li-Chang Cheng 1, Tao Jiang 1 and Thomas Girke 2,*

1Department of Computer Science and Engineering, University of California Riverside,
2Department of Botany and Plant Sciences, University of California Riverside

*To whom correspondence should be addressed. Dr. Thomas Girke, E-mail: thomas.girke{at}ucr.edu


  Abstract

Motivation: Software applications for structural similarity searching and clustering of small molecules play an important role in drug discovery and chemical genomics. Here we present the first open-source compound mining framework for the popular statistical programming environment R. The integration with a powerful statistical environment maximizes the flexibility, expandability and programmability of the provided analysis functions.

Results: We discuss the algorithms and compound mining utilities provided by the R package ChemmineR. It contains functions for structural similarity searching, clustering of compound libraries with a wide spectrum of classification algorithms and various utilities for managing complex compound data. It also offers a wide range of visualization functions for compound clusters and chemical structures. The package is well integrated with the online ChemMine environment and allows bidirectional communications between the two services.

Availability: ChemmineR is freely available as an R package from the ChemMine project site: http://bioweb.ucr.edu/ChemMineV2/chemminer.

Contact: thomas.girke{at}ucr.edu

Associate Editor: Prof. Anna Tramontano

Received on April 21, 2008; revised on April 21, 2008; accepted on June 10, 2008

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