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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 |
| Reference manual: | wTO.pdf |
| 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 imports: | NetSci |
| Reverse suggests: | CoDiNA |
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