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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "corto" in publications use:'
type: software
license: LGPL-3.0-only
title: 'corto: Inference of Gene Regulatory Networks'
version: 1.2.2
doi: 10.1093/bioinformatics/btaa223
identifiers:
- type: doi
  value: 10.32614/CRAN.package.corto
abstract: 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 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) <https://doi.org/10.1093/bioinformatics/btaa223>.
authors:
- family-names: Giorgi
  given-names: Federico M.
  email: federico.giorgi@gmail.com
preferred-citation:
  type: article
  title: 'corto: a lightweight R package for gene network inference and master regulator
    analysis'
  authors:
  - family-names: Mercatelli
    given-names: Daniele
  - family-names: Lopez-Garcia
    given-names: Gonzalo
  - family-names: Giorgi
    given-names: Federico M
  journal: Bioinformatics
  year: '2020'
  month: '6'
  volume: '36'
  issue: '12'
  doi: 10.1093/bioinformatics/btaa223
  start: 3916-3917
repository: https://federicogiorgi.r-universe.dev
commit: f959be5e3b41049f23ad93a255ee19941a2bb111
contact:
- family-names: Giorgi
  given-names: Federico M.
  email: federico.giorgi@gmail.com