corto: Inference of Gene Regulatory Networks

We present 'corto' (Correlation Tool), a simple package to infer gene regulatory networks using DPI (Data Processing Inequality) and bootstrapping to recover edges. An initial step is performed to calculate all significant edges between a list of source nodes (centroids) and target genes. Then all triplets containing two centroids and one target are tested in a DPI step which removes edges. A bootstrapping process then calculates the robustness of the network, eventually re-adding edges previously removed by DPI. The package implements a similar pipeline as ARACNe-AP (Algorithm for the Reconstruction of Accurate Cellular Networks with Adaptive Partitioning) by Giorgi (2016) <doi:10.1093/bioinformatics/btw216>) with optimizations to run outside a computing cluster (most notably correlation to infer feature dependencies instead of Mutual Information).

Version: 0.99.10
Depends: R (≥ 3.5)
Imports: dplyr, knitr, parallel, pbapply, rmarkdown, stats, utils
Published: 2019-10-30
Author: Federico M. Giorgi [aut, cre], Daniele Mercatelli [ctb], Gonzalo Lopez-Garcia [ctb]
Maintainer: Federico M. Giorgi <federico.giorgi at gmail.com>
License: LGPL-3
NeedsCompilation: no
Citation: corto citation info
Materials: README
CRAN checks: corto results

Downloads:

Reference manual: corto.pdf
Vignettes: corto_vignette
Package source: corto_0.99.10.tar.gz
Windows binaries: r-devel: corto_0.99.10.zip, r-devel-gcc8: corto_0.99.10.zip, r-release: corto_0.99.10.zip, r-oldrel: corto_0.99.10.zip
OS X binaries: r-release: corto_0.99.10.tgz, r-oldrel: corto_0.99.10.tgz

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