Package: corto
Type: Package
Title: Inference of Gene Regulatory Networks
Version: 1.0.2
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"))
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 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).
License: LGPL-3
Encoding: UTF-8
LazyData: TRUE
RoxygenNote: 7.0.2
Depends: R (>= 3.6)
NeedsCompilation: no
Imports: dplyr, knitr, parallel, pbapply, plotrix, rmarkdown, stats,
        utils
VignetteBuilder: knitr
Packaged: 2020-01-30 11:44:22 UTC; Utente
Author: Federico M. Giorgi [aut, cre],
  Daniele Mercatelli [ctb],
  Gonzalo Lopez-Garcia [ctb]
Repository: CRAN
Date/Publication: 2020-01-30 12:00:05 UTC
