# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "TENET" in publications use:'
type: software
license: GPL-2.0-only
title: 'TENET: R package for TENET (Tracing regulatory Element Networks using Epigenetic
  Traits) to identify key transcription factors'
version: 1.5.0
doi: 10.1093/bioinformatics/btaf435
identifiers:
- type: doi
  value: 10.32614/CRAN.package.TENET
abstract: TENET identifies key transcription factors (TFs) and regulatory elements
  (REs) linked to a specific cell type by finding significantly correlated differences
  in gene expression and RE DNA methylation between case and control input datasets,
  and identifying the top genes by number of significant RE DNA methylation site links.
  It also includes many tools for visualization and analysis of the results, including
  plots displaying and comparing methylation and expression data and methylation site
  link counts, survival analysis, TF motif searching in the vicinity of linked RE
  DNA methylation sites, custom TAD and peak overlap analysis, and UCSC Genome Browser
  track file generation. A utility function is also provided to download methylation,
  expression, and patient survival data from The Cancer Genome Atlas (TCGA) for use
  in TENET or other analyses.
authors:
- name: Rhie Lab at the University of Southern California
  email: rhielab@gmail.com
- family-names: Mullen
  given-names: Daniel
  orcid: https://orcid.org/0000-0002-7639-0549
- family-names: Wu
  given-names: Zexun
  orcid: https://orcid.org/0000-0003-2566-1326
- family-names: Nelson-Moore
  given-names: Ethan
  orcid: https://orcid.org/0009-0001-6903-9232
- family-names: Rhie
  given-names: Suhn
  orcid: https://orcid.org/0000-0002-5522-5296
preferred-citation:
  type: article
  title: 'Tracing regulatory element networks using epigenetic traits to identify
    key transcription factors: TENET R/Bioconductor package'
  authors:
  - family-names: Mullen
    given-names: Daniel J
  - family-names: Wu
    given-names: Zexun
    orcid: https://orcid.org/0000-0003-2566-1326
  - family-names: Nelson-Moore
    given-names: Ethan
    orcid: https://orcid.org/0009-0001-6903-9232
  - family-names: Cao
    given-names: Huan
  - family-names: Han
    given-names: Lauren
  - family-names: Offringa
    given-names: Ite A
  - family-names: Rhie
    given-names: Suhn K
    email: rhie@usc.edu
    orcid: https://orcid.org/0000-0002-5522-5296
  journal: Bioinformatics
  year: '2025'
  volume: '41'
  issue: btaf435
  doi: 10.1093/bioinformatics/btaf435
  url: https://doi.org/10.1093/bioinformatics/btaf435
repository: https://bioc.r-universe.dev
repository-code: https://github.com/rhielab/TENET
commit: a1cd8ef1918b8a9cb0cff3fbbe4b850fdda54473
url: https://github.com/rhielab/TENET
date-released: '2026-04-28'
contact:
- name: Rhie Lab at the University of Southern California
  email: rhielab@gmail.com