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# CITATION.cff file created with {cffr} R package
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cff-version: 1.2.0
message: 'To cite package "epiPortrait" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'epiPortrait: Replicate-Aware Epigenomic Domain Profiling'
version: 0.99.3
doi: 10.32614/CRAN.package.epiPortrait
abstract: Provides methods for replicate-aware quantitative phenotyping and comparison
  of epigenomic domains from normalized continuous signal tracks and per-sample native
  peak/domain calls (histone-mark ChIP-seq / CUT&Tag as the primary use case; also
  applicable to ATAC-seq-derived domains). It characterizes each shared genomic domain
  by integrated signal magnitude (Intensity), sample-specific native peak breadth
  geometry, and continuous within-domain signal architecture (SignalDispersion). Replicate-level
  evidence is retained and aggregated with specified support rules, enabling condition-specific
  classification of Intensity-Super, Breadth-Super, Dual-Super, Typical, or Uncertain
  domain states without using the consensus-domain width as the breadth caller. The
  package further supports condition transitions, continuous domain-width remodeling,
  signal quality control, genome-aware domain annotation with a three-level export
  (per-domain summary, per-domain-gene pair, and raw relationship detail), optional
  BEDPE contact evidence, expression-aware candidate-gene prioritization, differential
  domain analysis on continuous BigWig signal using limma, and result visualization.
authors:
- family-names: ZHANG
  given-names: Ying
  email: 12207129@zju.edu.cn
  orcid: https://orcid.org/0009-0005-9644-7062
repository: https://biocstaging.r-universe.dev
repository-code: https://github.com/zying106/epiPortrait
commit: 6dd14984eba9dfb38708b30501b2edd85b6dcbf9
url: https://github.com/zying106/epiPortrait
date-released: '2026-09-04'
contact:
- family-names: ZHANG
  given-names: Ying
  email: 12207129@zju.edu.cn
  orcid: https://orcid.org/0009-0005-9644-7062