ChemmineR: a compound mining framework for R.
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
Cao
Yiqun
Y
Department of Computer Science and Engineering, University of California, Riverside, California, USA.
Charisi
Anna
A
Cheng
Li-Chang
LC
Jiang
Tao
T
Girke
Thomas
T
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
D001704:Biopolymers