# --------------------------------------------
# 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 "BiRewire" in publications use:'
type: software
license: GPL-3.0-only
title: 'BiRewire: High-performing routines for the randomization of a bipartite graph
  (or a binary event matrix), undirected and directed signed graph preserving degree
  distribution (or marginal totals)'
version: 3.37.0
abstract: 'Fast functions for bipartite network rewiring through N consecutive switching
  steps (See References) and for the computation of the minimal number of switching
  steps to be performed in order to maximise the dissimilarity with respect to the
  original network. Includes functions for the analysis of the introduced randomness
  across the switching steps and several other routines to analyse the resulting networks
  and their natural projections. Extension to undirected networks and directed signed
  networks is also provided. Starting from version 1.9.7 a more precise bound (especially
  for small network) has been implemented. Starting from version 2.2.0 the analysis
  routine is more complete and a visual montioring of the underlying Markov Chain
  has been implemented. Starting from 3.6.0 the library can handle also matrices with
  NA (not for the directed signed graphs). Since version 3.27.1 it is possible to
  add a constraint for dsg generation: usually positive and negative arc between two
  nodes could be not accepted.'
authors:
- family-names: Gobbi
  given-names: Andrea
  email: gobbi.andrea@mail.com
- family-names: Iorio
  given-names: Francesco
- family-names: Jurman
  given-names: Giuseppe
- family-names: Albanese
  given-names: Davide
- family-names: Saez-Rodriguez.
  given-names: Julio
preferred-citation:
  type: manual
  title: 'BiRewire: High-performing routines for the randomization of a bipartite
    graph (or a binary event matrix), undirected and directed signed graph preserving
    degree distribution (or marginal totals)'
  authors:
  - family-names: Gobbi
    given-names: A.
  - family-names: Iorio
    given-names: F.
  - family-names: Albanese
    given-names: D.
  - family-names: Jurman
    given-names: G
  - family-names: Saez-Rodriguez
    given-names: J.
  year: '2022'
  notes: R package version 3.37.0
  url: https://www.bioconductor.org/packages/release/bioc/html/BiRewire.html
repository: https://bioc.r-universe.dev
url: http://www.ebi.ac.uk/~iorio/BiRewire
date-released: '2022-02-10'
contact:
- family-names: Gobbi
  given-names: Andrea
  email: gobbi.andrea@mail.com
references:
- type: article
  title: Fast randomization of large genomic datasets while preserving alteration
    counts
  authors:
  - family-names: Gobbi
    given-names: A.
  - family-names: Iorio
    given-names: F.
  - family-names: Dawson
    given-names: K.J.
  - family-names: Wedge
    given-names: D.C.
  - family-names: Tamborero
    given-names: D.
  - family-names: Alexandrov
    given-names: L.
  - family-names: Lopez-Bigas
    given-names: N.
  - family-names: Garnett
    given-names: M.J.
  - family-names: Jurman
    given-names: G
  - family-names: Saez-Rodriguez
    given-names: J.
  doi: 10.1093/bioinformatics/btu474
  journal: BMC Bioinformatics
  issue: '17'
  volume: '30'
  year: '2014'
  url: http://bioinformatics.oxfordjournals.org/content/30/17/i617.full.pdf+html
  start: 617-623
- type: article
  title: Efficient randomization of biologicalnetworks while preserving functionalcharacterization
    of individual nodes
  authors:
  - family-names: Iorio
    given-names: F.
  - family-names: Bernardo-Faura
    given-names: M.
  - family-names: Gobbi
    given-names: A.
  - family-names: Cokelaer
    given-names: T.
  - family-names: Jurman
    given-names: G
  - family-names: Saez-Rodriguez
    given-names: J.
  doi: 10.1186/s12859-016-1402-1
  journal: BMC Bioinformatics
  issue: '1'
  volume: '17'
  year: '542'
  url: http://dx.doi.org/10.1186/s12859-016-1402-1
  start: 617-623