cooccurNet: an R package for co-occurrence network construction and analysis
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.Availability and Implementation:
‘cooccurNet’ is publicly available on CRAN repositories under the GPL-3 Open Source License (http://cran.r-project.org/package=cooccurNet)Contact:
email@example.com or firstname.lastname@example.orgSupplementary information:
Supplementary data are available at Bioinformatics online.