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 |
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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