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 a DPI step removes edges: by default, for each target only the edge
from the centroid with the strongest correlation is kept; optionally, the
ARACNe rule removes an edge only if it is the weakest in a triplet of two
centroids and one target. A bootstrapping process then calculates
the robustness of the network, eventually re-adding edges previously removed by DPI.
The algorithm has been optimized to run outside a computing cluster, using a fast correlation
implementation. The package finally provides functions to calculate network enrichment
analysis from RNA-Seq and ATAC-Seq signatures as described in the article by
Giorgi lab (2020) <doi:10.1093/bioinformatics/btaa223>.
| Version: |
1.4.0 |
| Depends: |
R (≥ 3.6) |
| Imports: |
grDevices, graphics, methods, parallel, pbapply, plotrix, stats, utils |
| Suggests: |
knitr, rmarkdown |
| Published: |
2026-10-21 |
| DOI: |
10.32614/CRAN.package.corto |
| Author: |
Federico M. Giorgi [aut, cre],
Daniele Mercatelli [ctb],
Gonzalo Lopez-Garcia [ctb],
Hugo Tovar [ctb],
Hualin Wang [ctb] |
| Maintainer: |
Federico M. Giorgi <federico.giorgi at gmail.com> |
| License: |
LGPL-3 |
| NeedsCompilation: |
no |
| Citation: |
corto citation info |
| Materials: |
NEWS |
| CRAN checks: |
corto results |
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