corto: Inference of Gene Regulatory Networks

We present 'corto' (Correlation Tool), a simple package to infer gene regulatory networks and visualize master regulators from gene expression data 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: 1.0.2
Depends: R (≥ 3.6)
Imports: dplyr, knitr, parallel, pbapply, plotrix, rmarkdown, stats, utils
Published: 2020-01-30
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_1.0.2.tar.gz
Windows binaries: r-devel: corto_1.0.2.zip, r-devel-gcc8: corto_0.99.10.zip, r-release: corto_1.0.2.zip, r-oldrel: corto_0.99.10.zip
OS X binaries: r-release: corto_1.0.2.tgz, r-oldrel: corto_0.99.10.tgz
Old sources: corto archive

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