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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 "epiregulon" in publications use:'
type: software
license: MIT
title: 'epiregulon: Gene regulatory network inference from single cell epigenomic
  data'
version: 1.1.2
doi: 10.1101/2023.11.27.568955
abstract: Gene regulatory networks model the underlying gene regulation hierarchies
  that drive gene expression and observed phenotypes. Epiregulon infers TF activity
  in single cells by constructing a gene regulatory network (regulons). This is achieved
  through integration of scATAC-seq and scRNA-seq data and incorporation of public
  bulk TF ChIP-seq data. Links between regulatory elements and their target genes
  are established by computing correlations between chromatin accessibility and gene
  expressions.
authors:
- family-names: Yao
  given-names: Xiaosai
  email: xiaosai.yao@gmail.com
  orcid: https://orcid.org/0000-0001-9729-0726
- family-names: Włodarczyk
  given-names: Tomasz
  email: tomwlo@gmail.com
  orcid: https://orcid.org/0000-0003-1554-9699
- family-names: Lun
  given-names: Aaron
  email: infinite.monkeys.with.keyboards@gmail.com
- family-names: Chen
  given-names: Shang-Yang
  email: sychen9584@gmail.com
preferred-citation:
  type: article
  title: 'Epiregulon: Inference of single-cell transcription factor activity to dissect
    mechanisms of lineage plasticity and drug response'
  authors:
  - family-names: Wlodarczyk
    given-names: Tomasz
  - family-names: Lun
    given-names: Aaron
    email: infinite.monkeys.with.keyboards@gmail.com
  - family-names: Wu
    given-names: Diana
  - family-names: Menon
    given-names: Shreya
  - family-names: Toneyan
    given-names: Shushan
  - family-names: Seidel
    given-names: Kerstin
  - family-names: Wang
    given-names: Liang
  - family-names: Tan
    given-names: Jenille
  - family-names: Chen
    given-names: Shang-Yang
    email: sychen9584@gmail.com
  - family-names: Keyes
    given-names: Timothy
  - family-names: Chlebowski
    given-names: Aleksander
  - family-names: Guo
    given-names: Yu
  - family-names: Metcalfe
    given-names: Ciara
  - family-names: Hafner
    given-names: Marc
  - family-names: Siebel
    given-names: Christian W.
  - family-names: Corces
    given-names: M. Ryan
  - family-names: Yauch
    given-names: Robert
  - family-names: Xie
    given-names: Shiqi
  - family-names: Yao
    given-names: Xiaosai
    email: xiaosai.yao@gmail.com
    orcid: https://orcid.org/0000-0001-9729-0726
  journal: bioRxiv
  year: '2023'
  doi: 10.1101/2023.11.27.568955
repository: https://bioc.r-universe.dev
repository-code: https://github.com/xiaosaiyao/epiregulon
url: https://github.com/xiaosaiyao/epiregulon/
date-released: '2024-06-13'
contact:
- family-names: Yao
  given-names: Xiaosai
  email: xiaosai.yao@gmail.com
  orcid: https://orcid.org/0000-0001-9729-0726