title: ChemmineR: a compound mining framework for R.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  ChemmineR is freely available as an R package from the ChemMine project site: http://bioweb.ucr.edu/ChemMineV2/chemminer
authors.affiliation: Department of Computer Science and Engineering, University of California, Riverside, California, USA.
authors.forename: Yiqun
authors.initials: Y
authors.lastname: Cao
authors.forename: Anna
authors.initials: A
authors.lastname: Charisi
authors.forename: Li-Chang
authors.initials: LC
authors.lastname: Cheng
authors.forename: Tao
authors.initials: T
authors.lastname: Jiang
authors.forename: Thomas
authors.initials: T
authors.lastname: Girke
mesh_terms: D000465:Algorithms; D001704:Biopolymers / Q000737:chemistry*; D003628:Database Management Systems; D016208:Databases, Factual; D016247:Information Storage and Retrieval / Q000379:methods*; D011381:Programming Languages; D012984:Software
chemical_list: D001704:Biopolymers