ChemmineR: a compound mining framework for R
Open Access
- 2 July 2008
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 24 (15), 1733-1734
- https://doi.org/10.1093/bioinformatics/btn307
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:thomas.girke@ucr.eduKeywords
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