Imports: Rdpack, methods, purrr, nloptr, osqp, Rcpp, furrr (>= 0.2.0)

Title: Inference of Gene Regulatory Networks
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).
Imports: dplyr, knitr, parallel, pbapply, rmarkdown, stats, utils

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
Imports: dplyr, knitr, parallel, pbapply, plotrix, rmarkdown, stats,

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 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

Imports: dplyr, gplots, knitr, parallel, pbapply, plotrix, rmarkdown,
Packaged: 2021-10-22 12:12:47 UTC; federico.giorgi4

Imports: dplyr, gplots, knitr, methods, parallel, pbapply, plotrix,
Packaged: 2022-05-23 15:09:20 UTC; federico.giorgi4