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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: 1.1.0
doi: 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
repository: https://bioc.r-universe.dev
repository-code: https://github.com/Egors01/DuplexDiscovereR/issues/
commit: 37477e10cc8137ff130f14ec40e1c062fafe0a93
url: https://github.com/Egors01/DuplexDiscovereR/
contact:
- family-names: Semenchenko
  given-names: Egor
  email: yegor.smb@gmail.com
  orcid: https://orcid.org/0009-0007-5306-076X