cooccurNet: an R package for co-occurrence network construction and analysis

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Abstract

Motivation:

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:

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

Supplementary information:

Supplementary data are available at Bioinformatics online.

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