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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 "EpiCompare" in publications use:'
type: software
license: GPL-3.0-only
title: 'EpiCompare: Comparison, Benchmarking & QC of Epigenomic Datasets'
version: 1.9.2
abstract: 'EpiCompare is used to compare and analyse epigenetic datasets for quality
  control and benchmarking purposes. The package outputs an HTML report consisting
  of three sections: (1. General metrics) Metrics on peaks (percentage of blacklisted
  and non-standard peaks, and peak widths) and fragments (duplication rate) of samples,
  (2. Peak overlap) Percentage and statistical significance of overlapping and non-overlapping
  peaks. Also includes upset plot and (3. Functional annotation) functional annotation
  (ChromHMM, ChIPseeker and enrichment analysis) of peaks. Also includes peak enrichment
  around TSS.'
authors:
- family-names: Choi
  given-names: Sera
  email: serachoi1230@gmail.com
  orcid: https://orcid.org/0000-0002-5077-1984
- family-names: Schilder
  given-names: Brian
  email: brian_schilder@alumni.brown.edu
  orcid: https://orcid.org/0000-0001-5949-2191
- family-names: Abbasova
  given-names: Leyla
  email: profernitsky@gmail.com
- family-names: Murphy
  given-names: Alan
  email: alanmurph94@hotmail.com
  orcid: https://orcid.org/0000-0002-2487-8753
- family-names: Roberts
  given-names: Thomas
  email: tomroberts.work15@gmail.com
- family-names: Skene
  given-names: Nathan
  email: nathan.skene@gmail.com
  orcid: https://orcid.org/0000-0002-6807-3180
preferred-citation:
  type: article
  title: 'EpiCompare: R package for the comparison and quality control of epigenomic
    peak files'
  authors:
  - family-names: Choi
    given-names: Sera
    email: serachoi1230@gmail.com
    orcid: https://orcid.org/0000-0002-5077-1984
  - family-names: Schilder
    given-names: Brian M.
  - family-names: Abbasova
    given-names: Leyla
    email: profernitsky@gmail.com
  - family-names: Murphy
    given-names: Alan E.
  - family-names: Skene
    given-names: Nathan G.
  journal: bioRxiv
  year: '2022'
  url: https://doi.org/10.1101/2022.07.22.501149
repository: https://bioc.r-universe.dev
repository-code: https://github.com/neurogenomics/EpiCompare
url: https://github.com/neurogenomics/EpiCompare
contact:
- family-names: Roberts
  given-names: Thomas
  email: tomroberts.work15@gmail.com