cooccurNet: an R package for co-occurrence network construction and analysis.
BACKGROUND
Previously, we developed a computational model to identify genomic co-occurrence networks that was applied to capture the coevolution patterns within genomes of influenza viruses. To facilitate easy public use of this model, an R package 'cooccurNet' is presented here.


RESULTS
'cooccurNet' includes functionalities of construction and analysis of residues (e.g. nucleotides, amino acids and SNPs) co-occurrence network. In addition, a new method for measuring residues coevolution, defined as residue co-occurrence score (RCOS), is proposed and implemented in 'cooccurNet' based on the co-occurrence network.


METHODS
'cooccurNet' is publicly available on CRAN repositories under the GPL-3 Open Source License ( http://cran.r-project.org/package=cooccurNet ).


BACKGROUND
taijiao@ibms.pumc.edu.cn or pys2013@hnu.edu.cn.


BACKGROUND
Supplementary data are available at Bioinformatics online.
College of Computer Science and Electronic Engineering, Hunan University, Changsha, China.
Yuanqiang
Y
Zou
College of Computer Science and Electronic Engineering, Hunan University, Changsha, China.
Zhiqiang
Z
Wu
Center of System Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.|Suzhou Institute of Systems Medicine, Suzhou, China.
Lizong
L
Deng
Center of System Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.|Suzhou Institute of Systems Medicine, Suzhou, China.
Aiping
A
Wu
College of Computer Science and Electronic Engineering, Hunan University, Changsha, China.
Fan
F
Wu
College of Computer Science and Electronic Engineering, Hunan University, Changsha, China.
Kenli
K
Li
Center of System Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.|Suzhou Institute of Systems Medicine, Suzhou, China.
Taijiao
T
Jiang
College of Biology, Hunan University, Changsha, China.
Yousong
Y
Peng
D003198:Computer Simulation; D019143:Evolution, Molecular; D016679:Genome, Viral; D023281:Genomics / Q000379:methods*; D009975:Orthomyxoviridae / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D012984:Software