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cooccurNet: an R package for co-occurrence network construction and analysis
Yuanqiang Zou1, Zhiqiang Wu1, Lizong Deng2,3
1College of Computer Science and Electronic Engineering, Hunan University, Changsha, China.
Bioinformatics (Oxford, England)
|February 9, 2017
Summary
The cooccurNet R package simplifies identifying genomic co-occurrence networks and analyzing residue coevolution using a novel residue co-occurrence score (RCOS). This tool aids in understanding evolutionary patterns in viral genomes.
Area of Science:
- Computational Biology
- Bioinformatics
- Genomics
Background:
- A computational model was previously developed to identify genomic co-occurrence networks.
- This model was applied to capture coevolution patterns in influenza virus genomes.
Purpose of the Study:
- To present the R package 'cooccurNet' for public use.
- To facilitate the application of the genomic co-occurrence network model.
Main Methods:
- The 'cooccurNet' R package provides functionalities for constructing and analyzing residue co-occurrence networks.
- It implements a new method, the residue co-occurrence score (RCOS), to measure residue coevolution.
Main Results:
- 'cooccurNet' enables the analysis of co-occurrence networks for various residues, including nucleotides, amino acids, and SNPs.
- The package introduces and applies the novel RCOS metric for quantifying residue coevolution.
Conclusions:
- 'cooccurNet' offers a user-friendly tool for analyzing genomic co-occurrence and residue coevolution.
- The R package is available on CRAN under the GPL-3 Open Source License.
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