ChemmineR: A Compound Mining Framework for R. Export

@article{citeulike:2965276, 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@ucr.edu.}, address = {Department of Computer Science and Engineering, University of California Riverside.}, author = {Cao, Yiqun and Charisi, Anna and Cheng, Li-Chang C. and Jiang, Tao and Girke, Thomas}, citeulike-article-id = {2965276}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btn307}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/15/1733}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18596077}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18596077}, day = {2}, doi = {10.1093/bioinformatics/btn307}, issn = {1460-2059}, journal = {Bioinformatics (Oxford, England)}, keywords = {cheminformatics, data, gi, mining, package, r}, month = {July}, posted-at = {2008-08-05 18:20:45}, priority = {0}, title = {ChemmineR: A Compound Mining Framework for R.}, url = {http://dx.doi.org/10.1093/bioinformatics/btn307}, year = {2008} }

TY - JOUR ID - citeulike:2965276 L3 - citeulike-article-id:2965276 N2 - 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@ucr.edu. JF - Bioinformatics (Oxford, England) SN - 1460-2059 AD - Department of Computer Science and Engineering, University of California Riverside. TI - ChemmineR: A Compound Mining Framework for R. KW - cheminformatics KW - data KW - gi KW - mining KW - package KW - r AU - Cao, Yiqun AU - Charisi, Anna AU - Cheng, Li-Chang AU - Jiang, Tao AU - Girke, Thomas PY - 2008/07/02/ UR - http://dx.doi.org/10.1093/bioinformatics/btn307 ER -