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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 "HiCcompare" in publications use:'
type: software
license: MIT
title: 'HiCcompare: HiCcompare: Joint normalization and comparative analysis of multiple
  Hi-C datasets'
version: 1.27.0
doi: 10.1186/s12859-018-2288-x
abstract: HiCcompare provides functions for joint normalization and difference detection
  in multiple Hi-C datasets. HiCcompare operates on processed Hi-C data in the form
  of chromosome-specific chromatin interaction matrices. It accepts three-column tab-separated
  text files storing chromatin interaction matrices in a sparse matrix format which
  are available from several sources. HiCcompare is designed to give the user the
  ability to perform a comparative analysis on the 3-Dimensional structure of the
  genomes of cells in different biological states.`HiCcompare` differs from other
  packages that attempt to compare Hi-C data in that it works on processed data in
  chromatin interaction matrix format instead of pre-processed sequencing data. In
  addition, `HiCcompare` provides a non-parametric method for the joint normalization
  and removal of biases between two Hi-C datasets for the purpose of comparative analysis.
  `HiCcompare` also provides a simple yet robust method for detecting differences
  between Hi-C datasets.
authors:
- family-names: Dozmorov
  given-names: Mikhail
  email: mikhail.dozmorov@gmail.com
  orcid: https://orcid.org/0000-0002-0086-8358
- family-names: Cresswell
  given-names: Kellen
  email: cresswellkg@vcu.edu
- family-names: Stansfield
  given-names: John
  email: stansfieldjc@vcu.edu
preferred-citation:
  type: article
  title: 'HiCcompare: an R-package for joint normalization and comparison of HI-C
    datasets'
  authors:
  - family-names: Stansfield
    given-names: John C.
  - family-names: Cresswell
    given-names: Kellen G.
  - family-names: Vladimirov
    given-names: Vladimir I.
  - family-names: Dozmorov
    given-names: Mikhail G.
  journal: BMC Bioinformatics
  year: '2018'
  volume: '19'
  issue: '1'
  month: '12'
  url: https://github.com/dozmorovlab/HiCcompare
  doi: 10.1186/s12859-018-2288-x
repository: https://bioc.r-universe.dev
repository-code: https://github.com/dozmorovlab/HiCcompare
url: https://github.com/dozmorovlab/HiCcompare
contact:
- family-names: Dozmorov
  given-names: Mikhail
  email: mikhail.dozmorov@gmail.com
  orcid: https://orcid.org/0000-0002-0086-8358