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. 2008 Aug 1;24(15):1733-4.
doi: 10.1093/bioinformatics/btn307. Epub 2008 Jul 2.

ChemmineR: a compound mining framework for R

Yiqun Cao  1 , Anna Charisi, Li-Chang Cheng, Tao Jiang, Thomas Girke
Affiliations

ChemmineR: a compound mining framework for R

Yiqun Cao et al. Bioinformatics. .

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

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