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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 "CleanUpRNAseq" in publications use:'
type: software
license: GPL-3.0-only
title: 'CleanUpRNAseq: Detect and Correct Genomic DNA Contamination in RNA-seq Data'
version: 1.6.0
doi: 10.3390/biotech13030030
identifiers:
- type: doi
  value: 10.32614/CRAN.package.CleanUpRNAseq
abstract: RNA-seq data generated by some library preparation methods, such as rRNA-depletion-based
  method and the SMART-seq method, might be contaminated by genomic DNA (gDNA), if
  DNase I disgestion is not performed properly during RNA preparation. CleanUpRNAseq
  is developed to check if RNA-seq data is suffered from gDNA contamination. If so,
  it can perform correction for gDNA contamination and reduce false discovery rate
  of differentially expressed genes.
authors:
- family-names: Liu
  given-names: Haibo
  email: haibo.liu@umassmed.edu
  orcid: https://orcid.org/0000-0002-4213-2883
- family-names: Zhu
  given-names: Lihua Julie
  email: Julie.Zhu@umassmed.edu
- family-names: Hu
  given-names: Kai
  email: kai.hu@umassmed.edu
preferred-citation:
  type: article
  title: 'CleanUpRNAseq: An R/Bioconductor Package for Detecting and Correcting DNA
    Contamination in RNA-Seq Data'
  authors:
  - family-names: Liu
    given-names: Haibo
    email: haibo.liu@umassmed.edu
    orcid: https://orcid.org/0000-0002-4213-2883
  - family-names: Hu
    given-names: Kai
    email: kai.hu@umassmed.edu
  - family-names: O’Connor
    given-names: Kevin
  - family-names: Kelliher
    given-names: Michelle A.
  - family-names: Zhu
    given-names: Lihua Julie
    email: Julie.Zhu@umassmed.edu
  journal: BioTech
  year: '2024'
  volume: '13'
  issue: '3'
  doi: 10.3390/biotech13030030
  start: '30'
repository: https://bioc-release.r-universe.dev
repository-code: https://github.com/haibol2016/CleanUpRNAseq
commit: 769640e8832c7c57d1428395dd9e2973048aabcd
url: https://github.com/haibol2016/CleanUpRNAseq
date-released: '2026-04-28'
contact:
- family-names: Liu
  given-names: Haibo
  email: haibo.liu@umassmed.edu
  orcid: https://orcid.org/0000-0002-4213-2883