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BioMedR: an R/CRAN package for integrated data analysis pipeline in biomedical study
Jie Dong1,2, Min-Feng Zhu2, Yong-Huan Yun3
1National Engineering Laboratory for Deep Processing of Rice and Byproducts, Hunan Key Laboratory of Processed Food for Special Medical Purpose, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha,410003 P. R. China.
BioMedR is a new R package that provides molecular representations for chemicals, proteins, and DNA. This tool supports data mining by offering various descriptors, fingerprints, and analysis pipelines for biomedical research.
Area of Science:
- Bioinformatics
- Cheminformatics
- Computational Biology
Background:
- Explosive growth in publicly available chemistry and biology data necessitates effective data mining.
- A key challenge is representing diverse molecular objects (chemicals, proteins, DNA, interactions) for data mining.
- An integrated toolkit is needed to represent molecular objects and support data mining algorithms.
Purpose of the Study:
- To develop an integrated R package for molecular representations and data mining.
- To provide a comprehensive toolkit for cheminformatics and bioinformatics users.
Main Methods:
- Developed BioMedR, a freely available R/CRAN package.
- Implemented calculation of molecular descriptors and fingerprints for small molecules.
- Included protein descriptors, DNA descriptors, and interaction descriptors.
- Integrated similarity calculation methods and clustering algorithms.
Main Results:
- BioMedR calculates 293 molecular descriptors and 13 molecular fingerprints for small molecules.
- It computes 9920 protein descriptors and >6000 DNA descriptors.
- The package offers six types of generalized scale-based descriptors and six interaction descriptor types.
- Includes five similarity methods, four clustering algorithms, and auxiliary tools for an analysis pipeline.
Conclusions:
- BioMedR offers a comprehensive and uniform R package for diverse molecular representations.
- It facilitates the integration of different molecular object representations.
- The package benefits cheminformatics, bioinformatics, and other biomedical researchers.
