wTO: Computing Weighted Topological Overlaps (wTO) & Consensus wTO Network

Computes the Weighted Topological Overlap with positive and negative signs (wTO) networks given a data frame containing the mRNA count/ expression/ abundance per sample, and a vector containing the interested nodes of interaction (a subset of the elements of the full data frame). It also computes the cut-off threshold or p-value based on the individuals bootstrap or the values reshuffle per individual. It also allows the construction of a consensus network, based on multiple wTO networks. The package includes a visualization tool for the networks. More about the methodology can be found at <doi:10.48550/arXiv.1711.04702>.

Version: 2.0.2
Imports: data.table, igraph, magrittr, plyr, parallel, som, visNetwork, reshape2, Rfast, HiClimR, methods
Suggests: knitr, rmarkdown
Published: 2023-03-22
Author: Deisy Morselli Gysi, Andre Voigt, Tiago Miranda Fragoso, Eivind Almaas and Katja Nowick.
Maintainer: Deisy Morselli Gysi <deisy.ccnr at gmail.com>
License: GPL-2
NeedsCompilation: no
Citation: wTO citation info
Materials: README
CRAN checks: wTO results


Reference manual: wTO.pdf


Package source: wTO_2.0.2.tar.gz
Windows binaries: r-devel: wTO_2.0.2.zip, r-release: wTO_2.0.2.zip, r-oldrel: wTO_2.0.2.zip
macOS binaries: r-release (arm64): wTO_2.0.2.tgz, r-oldrel (arm64): wTO_2.0.2.tgz, r-release (x86_64): wTO_2.0.2.tgz
Old sources: wTO archive

Reverse dependencies:

Reverse imports: NetSci
Reverse suggests: CoDiNA


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