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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 "DuplexDiscovereR" in publications use:'
type: software
license: GPL-3.0-only
title: 'DuplexDiscovereR: Analysis of the data from RNA duplex probing experiments'
version: 1.6.0
doi: 10.1093/nar/gkaf266
identifiers:
- type: doi
  value: 10.32614/CRAN.package.DuplexDiscovereR
abstract: DuplexDiscovereR is a package designed for analyzing data from RNA cross-linking
  and proximity ligation protocols such as SPLASH, PARIS, LIGR-seq, and others. DuplexDiscovereR
  accepts input in the form of chimerically or split-aligned reads. It includes procedures
  for alignment classification, filtering, and efficient clustering of individual
  chimeric reads into duplex groups (DGs). Once DGs are identified, the package predicts
  RNA duplex formation and their hybridization energies. Additional metrics, such
  as p-values for random ligation hypothesis or mean DG alignment scores, can be calculated
  to rank final set of RNA duplexes. Data from multiple experiments or replicates
  can be processed separately and further compared to check the reproducibility of
  the experimental method.
authors:
- family-names: Semenchenko
  given-names: Egor
  email: yegor.smb@gmail.com
  orcid: https://orcid.org/0009-0007-5306-076X
- family-names: Meyer
  given-names: Irmtraud M.
  email: irmtraud.m.meyer@cantab.net
  orcid: https://orcid.org/0000-0002-4048-3479
preferred-citation:
  type: article
  title: 'DuplexDiscovereR: a computational method for the analysis of experimental
    duplex RNA-RNA interaction data'
  authors:
  - family-names: E
    given-names: Semenchenko
  - family-names: V
    given-names: Tsybulsky
  - family-names: IM
    given-names: Meyer
  journal: Nucleic Acids Research
  year: '2025'
  url: https://doi.org/10.1093/nar/gkaf266
  doi: 10.1093/nar/gkaf266
repository: https://bioc-release.r-universe.dev
repository-code: https://github.com/Egors01/DuplexDiscovereR/issues/
commit: 6f2f2e9d95170bb05e2344d6385a940c45c98bbd
url: https://github.com/Egors01/DuplexDiscovereR/
date-released: '2026-04-28'
contact:
- family-names: Semenchenko
  given-names: Egor
  email: yegor.smb@gmail.com
  orcid: https://orcid.org/0009-0007-5306-076X