Package: corto
Type: Package
Title: Inference of Gene Regulatory Networks
Version: 0.99.10
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 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: 6.1.1
Depends: R (>= 3.5)
NeedsCompilation: no
Imports: dplyr, knitr, parallel, pbapply, rmarkdown, stats, utils
VignetteBuilder: knitr
Packaged: 2019-10-25 10:54:06 UTC; feder
Author: Federico M. Giorgi [aut, cre],
  Daniele Mercatelli [ctb],
  Gonzalo Lopez-Garcia [ctb]
Repository: CRAN
Date/Publication: 2019-10-30 17:00:14 UTC
Built: R 3.5.3; ; 2020-01-26 08:15:04 UTC; windows
