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) ) with optimizations to run outside a computing cluster (most notably correlation to infer feature dependencies instead of Mutual Information).


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install.packages("corto")

0.99.10 by Federico M. Giorgi, 18 days ago


Browse source code at https://github.com/cran/corto


Authors: Federico M. Giorgi [aut, cre] , Daniele Mercatelli [ctb] , Gonzalo Lopez-Garcia [ctb]


Documentation:   PDF Manual  


LGPL-3 license


Imports dplyr, knitr, parallel, pbapply, rmarkdown, stats, utils


See at CRAN