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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 "linkSet" in publications use:'
type: software
license: MIT
title: 'linkSet: Base Classes for Storing Genomic Link Data'
version: 1.1.0
doi: 10.32614/CRAN.package.linkSet
identifiers:
- type: url
  value: https://gilberthan1011.github.io/linkSet
abstract: Provides a comprehensive framework for representing, analyzing, and visualizing
  genomic interactions, particularly focusing on gene-enhancer relationships. The
  package extends the GenomicRanges infrastructure to handle paired genomic regions
  with specialized methods for chromatin interaction data from Hi-C, Promoter Capture
  Hi-C (PCHi-C), and single-cell ATAC-seq experiments. Key features include conversion
  from common interaction formats, annotation of promoters and enhancers, distance-based
  analyses, interaction strength metrics, statistical modeling using CHiCANE methodology,
  and tailored visualization tools. The package aims to standardize the representation
  of genomic interaction data while providing domain-specific functions not available
  in general genomic interaction packages.
authors:
- family-names: Han
  given-names: Gilbert
  email: GilbertHan1011@gmail.com
  orcid: https://orcid.org/0009-0000-0293-2467
repository: https://bioc.r-universe.dev
repository-code: https://github.com/GilbertHan1011/linkSet/issues/new
commit: bdadbdd362b9f200e14b5a7e144a7d13dd6a1881
url: https://github.com/GilbertHan1011/linkSet
date-released: '2025-10-29'
contact:
- family-names: Han
  given-names: Gilbert
  email: GilbertHan1011@gmail.com
  orcid: https://orcid.org/0009-0000-0293-2467