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Bioinformatics. Aug 1, 2008; 24(15): 1733–1734.
Published online Jul 2, 2008. doi:  10.1093/bioinformatics/btn307
PMCID: PMC2638865

ChemmineR: a compound mining framework for R

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 popularstatistical 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: ude.rcu@ekrig.samoht

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