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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 "QuaternaryProd" in publications use:'
type: software
title: 'QuaternaryProd: Computes the Quaternary Dot Product Scoring Statistic for
  Signed and Unsigned Causal Graphs'
version: 1.39.0
abstract: QuaternaryProd is an R package that performs causal reasoning on biological
  networks, including publicly available networks such as STRINGdb. QuaternaryProd
  is an open-source alternative to commercial products such as Inginuity Pathway Analysis.
  For a given a set of differentially expressed genes, QuaternaryProd computes the
  significance of upstream regulators in the network by performing causal reasoning
  using the Quaternary Dot Product Scoring Statistic (Quaternary Statistic), Ternary
  Dot product Scoring Statistic (Ternary Statistic) and Fisher's exact test (Enrichment
  test). The Quaternary Statistic handles signed, unsigned and ambiguous edges in
  the network. Ambiguity arises when the direction of causality is unknown, or when
  the source node (e.g., a protein) has edges with conflicting signs for the same
  target gene. On the other hand, the Ternary Statistic provides causal reasoning
  using the signed and unambiguous edges only. The Vignette provides more details
  on the Quaternary Statistic and illustrates an example of how to perform causal
  reasoning using STRINGdb.
authors:
- family-names: Fakhry
  given-names: Carl Tony
  email: cfakhry@cs.umb.edu
- family-names: Zarringhalam
  given-names: Kourosh
preferred-citation:
  type: article
  title: 'Interpreting transcriptional changes using causal graphs: new methods and
    their practical utility on public networks'
  authors:
  - family-names: Fakhry
    given-names: Carl Tony
    email: cfakhry@cs.umb.edu
  - family-names: Choudhary
    given-names: Paul
  - family-names: Gutteridge
    given-names: Alex
  - family-names: Sidders
    given-names: Ben
  - family-names: Chen
    given-names: Ping
  - family-names: Ziemek
    given-names: Daniel
  - family-names: Zarringhalam
    given-names: Kourosh
  journal: BMC Bioinformatics
  year: '2016'
  volume: '17'
repository: https://bioc.r-universe.dev
date-released: '2015-10-22'
contact:
- family-names: Fakhry
  given-names: Carl Tony
  email: cfakhry@cs.umb.edu
references:
- type: article
  title: 'STRING v9.1: protein-protein interaction networks, with increased coverage
    and integration.'
  authors:
  - family-names: al.
    given-names: Franceschini A et
  journal: Nucleic Acids Research (Database issue)
  year: '2013'
  volume: '41'