WTO: an R package for computing weighted topological overlap and a consensus network with integrated visualization tool.

ABSTRACT:

Background

Network analyses, such as of gene co-expression networks, metabolic networks and ecological networks have become a central approach for the systems-level study of biological data. Several software packages exist for generating and analyzing such networks, either from correlation scores or the absolute value of a transformed score called weighted topological overlap (wTO). However, since gene regulatory processes can up- or down-regulate genes, it is of great interest to explicitly consider both positive and negative correlations when constructing a gene co-expression network.

Results

Here, we present an R package for calculating the weighted topological overlap (wTO), that, in contrast to existing packages, explicitly addresses the sign of the wTO values, and is t

SUBMITTER: Gysi DM 

PROVIDER: S-EPMC6201546 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature