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:10.1186/s12859-018-2351-7>.

Version:	2.1
Imports:	data.table, igraph, magrittr, plyr, parallel, som, visNetwork, reshape2, Rfast, HiClimR, methods
Suggests:	knitr, rmarkdown
Published:	2024-07-04
DOI:	10.32614/CRAN.package.wTO
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

Documentation:

Reference manual:

wTO.html , wTO.pdf

Downloads:

Package source:	wTO_2.1.tar.gz
Windows binaries:	r-devel: wTO_2.1.zip, r-release: wTO_2.1.zip, r-oldrel: wTO_2.1.zip
macOS binaries:	r-release (arm64): wTO_2.1.tgz, r-oldrel (arm64): wTO_2.1.tgz, r-release (x86_64): wTO_2.1.tgz, r-oldrel (x86_64): wTO_2.1.tgz
Old sources:	wTO archive

Reverse dependencies:

Reverse imports:	NetSci
Reverse suggests:	CoDiNA

Linking:

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