Package: corto
Type: Package
Title: Inference of Gene Regulatory Networks
Version: 1.4.0
Authors@R: c(
 person("Federico M.","Giorgi",email = "federico.giorgi@gmail.com",role=c("aut","cre")),
 person("Daniele","Mercatelli",email = "danielemercatelli@gmail.com",role="ctb"),
 person("Gonzalo","Lopez-Garcia",email = "gonzolgarcia@gmail.com",role="ctb"),
 person("Hugo","Tovar",email = "hatovar@inmegen.gob.mx",role="ctb"),
 person("Hualin","Wang",email = "wanghualin@stu.njmu.edu.cn",role="ctb"))
Maintainer: Federico M. Giorgi <federico.giorgi@gmail.com>
Description: 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>.
License: LGPL-3
Encoding: UTF-8
Depends: R (>= 3.6)
NeedsCompilation: no
Imports: grDevices, graphics, methods, parallel, pbapply, plotrix,
        stats, utils
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Config/roxygen2/version: 8.1.0
Repository: https://federicogiorgi.r-universe.dev
Date/Publication: 2026-10-20 19:02:23 UTC
RemoteUrl: https://github.com/federicogiorgi/corto
RemoteRef: HEAD
RemoteSha: 132dcc6cfc571301ecdd3d3af50c9bab83fc3ca4
Packaged: 2026-10-20 20:13:16 UTC; root
Author: Federico M. Giorgi [aut, cre],
  Daniele Mercatelli [ctb],
  Gonzalo Lopez-Garcia [ctb],
  Hugo Tovar [ctb],
  Hualin Wang [ctb]