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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 "PICB" in publications use:'
type: software
license: CC0-1.0
title: 'PICB: piRNA Cluster Builder'
version: 0.99.15
doi: 10.1016/j.celrep.2024.114777
identifiers:
- type: doi
  value: 10.32614/CRAN.package.PICB
abstract: piRNAs (short for PIWI-interacting RNAs) and their PIWI protein partners
  play a key role in fertility and maintaining genome integrity by restricting mobile
  genetic elements (transposons) in germ cells. piRNAs originate from genomic regions
  known as piRNA clusters. The piRNA Cluster Builder (PICB) is a versatile toolkit
  designed to identify genomic regions with a high density of piRNAs. It constructs
  piRNA clusters through a stepwise integration of unique and multimapping piRNAs
  and offers wide-ranging parameter settings, supported by an optimization function
  that allows users to test different parameter combinations to tailor the analysis
  to their specific piRNA system. The output includes extensive metadata columns,
  enabling researchers to rank clusters and extract cluster characteristics.
authors:
- family-names: Genzor
  given-names: Pavol
- family-names: Friman
  given-names: Aleksandr
  email: haase-lab-bioinfo@nih.gov
- family-names: Stoyko
  given-names: Daniel
- family-names: Konstantinidou
  given-names: Parthena
  email: haase-lab-bioinfo@nih.gov
- family-names: Ahrend
  given-names: Franziska
  email: haase-lab-bioinfo@nih.gov
  orcid: https://orcid.org/0009-0004-7464-3444
- family-names: Loubalova
  given-names: Zuzana
  email: haase-lab-bioinfo@nih.gov
- family-names: Wang
  given-names: Yuejun
  email: haase-lab-bioinfo@nih.gov
- family-names: Lorenzi
  given-names: Hernan
  email: haase-lab-bioinfo@nih.gov
- family-names: Haase
  given-names: Astrid D
  email: haase-lab-bioinfo@nih.gov
preferred-citation:
  type: article
  title: A comparative roadmap of PIWI-interacting RNAs across seven species reveals
    insights into de novo piRNA-precursor formation in mammals
  authors:
  - family-names: Konstantinidou
    given-names: Parthena
    email: haase-lab-bioinfo@nih.gov
  - family-names: Loubalova
    given-names: Zuzana
    email: haase-lab-bioinfo@nih.gov
  - family-names: Ahrend
    given-names: Franziska
    email: haase-lab-bioinfo@nih.gov
    orcid: https://orcid.org/0009-0004-7464-3444
  - family-names: Friman
    given-names: Aleksandr
    email: haase-lab-bioinfo@nih.gov
  - family-names: Almeida
    given-names: Miguel Vasconcelos
  - family-names: Poulet
    given-names: Axel
  - family-names: Horvat
    given-names: Filip
  - family-names: Wang
    given-names: Yuejun
    email: haase-lab-bioinfo@nih.gov
  - family-names: Losert
    given-names: Wolfgang
  - family-names: Lorenzi
    given-names: Hernan
    email: haase-lab-bioinfo@nih.gov
  - family-names: Svoboda
    given-names: Petr
  - family-names: Miska
    given-names: Eric A.
  - family-names: Wolfswinkel
    given-names: Josien C.
    name-particle: van
  - family-names: Haase
    given-names: Astrid D.
  year: '2024'
  journal: Cell Reports
  volume: '43'
  issue: '10'
  publisher:
    name: Elsevier
  doi: 10.1016/j.celrep.2024.114777
  url: https://github.com/HaaseLab/PICB
  start: '114777'
repository: https://bioc.r-universe.dev
repository-code: https://github.com/HaaseLab/PICB
commit: 7163d82378d153d7913d042529a2d4fe0192d8e6
url: https://github.com/HaaseLab/PICB
contact:
- family-names: Ahrend
  given-names: Franziska
  email: haase-lab-bioinfo@nih.gov
  orcid: https://orcid.org/0009-0004-7464-3444