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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 "NADfinder" in publications use:'
type: software
license: GPL-2.0-or-later
title: 'NADfinder: Call wide peaks for sequencing data'
version: 1.36.0
identifiers:
- type: doi
  value: 10.32614/CRAN.package.NADfinder
abstract: Nucleolus is an important structure inside the nucleus in eukaryotic cells.
  It is the site for transcribing rDNA into rRNA and for assembling ribosomes, aka
  ribosome biogenesis. In addition, nucleoli are dynamic hubs through which numerous
  proteins shuttle and contact specific non-rDNA genomic loci. Deep sequencing analyses
  of DNA associated with isolated nucleoli (NAD- seq) have shown that specific loci,
  termed nucleolus- associated domains (NADs) form frequent three- dimensional associations
  with nucleoli. NAD-seq has been used to study the biological functions of NAD and
  the dynamics of NAD distribution during embryonic stem cell (ESC) differentiation.
  Here, we developed a Bioconductor package NADfinder for bioinformatic analysis of
  the NAD-seq data, including baseline correction, smoothing, normalization, peak
  calling, and annotation.
authors:
- family-names: Ou
  given-names: Jianhong
  email: jou@morgridge.org
- family-names: Zhu
  given-names: Lihua Julie
  email: julie.zhu@umassmed.edu
- family-names: Liu
  given-names: Haibo
- family-names: Yu
  given-names: Jun
- family-names: Pagès
  given-names: Hervé
- family-names: Kaufman
  given-names: Paul
preferred-citation:
  type: article
  title: Two Contrasting Classes of Nucleolus-Associated Domains in Mouse Fibroblast
    Heterochromatin
  authors:
  - family-names: Vertii
    given-names: Anastassiia
  - family-names: Ou
    given-names: Jianhong
    email: jou@morgridge.org
  - family-names: Yu
    given-names: Jun
  - family-names: Yan
    given-names: Aimin
  - family-names: Liu
    given-names: Haibo
  - family-names: Zhu
    given-names: Lihua Julie
    email: julie.zhu@umassmed.edu
  - family-names: Kaufman
    given-names: Paul D
  publisher:
    name: CSH publisher
  journal: Genome Research
  year: '2019'
  url: https://genome.cshlp.org/content/29/8/1235.full
repository: https://bioc-release.r-universe.dev
commit: 3c841fd0c980a5f063cf4159f29d935e9c367aa5
date-released: '2026-04-28'
contact:
- family-names: Ou
  given-names: Jianhong
  email: jou@morgridge.org
- family-names: Zhu
  given-names: Lihua Julie
  email: julie.zhu@umassmed.edu