Title

Authors

Affiliation

¹Department of Mathematics, University of Louisville, Louisville, KY 40292 USA; ²Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, KY 40292 USA

Email

susmita.datta@louisville.edu; *Corresponding author

Article Type

Software

Date

Received March 31, 2014; Accepted April 02, 2014; Published April 23, 2014

Differential network analysis provides a framework for examining if there is sufficient statistical evidence to conclude that the structure of a network differs under two experimental conditions or if the structures of two networks are different. The R package dna provides tools and procedures for differential network analysis of genomic data. The focus of this package is on gene-gene networks, but the methods are easily adaptable for more general biological processes. This package includes preprocessing tools for simultaneously preparing a pair of networks for analysis, procedures for computing connectivity scores between pairs of genes based on many available statistical techniques, and tools for handling modules of genes based on these scores. Also, procedures are provided for performing permutation tests based on these scores to determine if the connectivity of a gene differs between the two networks, to determine if the connectivity of a particular set of important genes differs between the two networks, and to determine if the overall module structure differs between the two networks. Several built-in options are available for the types of scores and distances used in the testing procedures, and additionally, the procedures provide flexible methods that allow the user to define custom scores and distances.

Availability

dna is freely available at The Comprehensive R Archive Network, http://CRAN.R-project.org/package=dna

Citation

Gill  et al. Bioinformation 10(4): 233-234 (2014)
 

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.