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2014 ; 10
(4
): 233-4
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dna: An R package for differential network analysis
#MMPMID24966526
Gill R
; Datta S
; Datta S
Bioinformation
2014[]; 10
(4
): 233-4
PMID24966526
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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.
free
free
free
