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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 "cleanUpdTSeq" in publications use:'
type: software
license: GPL-2.0-only
title: 'cleanUpdTSeq: cleanUpdTSeq cleans up artifacts from polyadenylation sites
  from oligo(dT)-mediated 3'' end RNA sequending data'
version: 1.43.0
doi: 10.1093/bioinformatics/btt446
abstract: This package implements a Naive Bayes classifier for accurately differentiating
  true polyadenylation sites (pA sites) from oligo(dT)-mediated 3' end sequencing
  such as PAS-Seq, PolyA-Seq and RNA-Seq by filtering out false polyadenylation sites,
  mainly due to oligo(dT)-mediated internal priming during reverse transcription.
  The classifer is highly accurate and outperforms other heuristic methods.
authors:
- email: Julie.Zhu@umassmed.edu
- family-names: Sheppard
  given-names: Sarah
- family-names: Liu
  given-names: Haibo
- family-names: Ou
  given-names: Jianhong
- family-names: Lawson
  given-names: Nathan
- family-names: Zhu
  given-names: Lihua Julie
preferred-citation:
  type: article
  title: Accurate identification of polyadenylation sites from 3' end deep sequencing
    using a naive Bayes classifier
  authors:
  - family-names: Sheppard
    given-names: Sarah
  - family-names: Lawson
    given-names: Nathan
  - family-names: Zhu
    given-names: Lihua
  journal: Bioinformatics
  volume: '29'
  year: '2013'
  issue: '20'
  url: http://bioinformatics.oxfordjournals.org/content/29/20/2564.long
  doi: 10.1093/bioinformatics/btt446
  issn: 1460-2059
  abstract: 'MOTIVATION: 3'' end processing is important for transcription termination,
    mRNA stability and regulation of gene expression. To identify 3'' ends, most techniques
    use an oligo-dT primer to construct deep sequencing libraries. However, this approach
    can lead to identification of artifactual polyadenylation sites due to internal
    priming in homopolymeric stretches of adenines. Although heuristic filters have
    been applied in these cases, they typically result in a high proportion of both
    false-positive and -negative classifications. Therefore, there is a need to develop
    improved algorithms to better identify mis-priming events in oligo-dT primed sequences.
    RESULTS: By analyzing sequence features flanking 3'' ends derived from oligo-dT-based
    sequencing, we developed a naive Bayes classifier to classify them as true or
    false/internally primed. The resulting algorithm is highly accurate, outperforms
    previous heuristic filters and facilitates identification of novel polyadenylation
    sites.'
  start: '2564'
repository: https://bioc.r-universe.dev
date-released: '2021-04-27'
contact:
- email: Julie.Zhu@umassmed.edu