Package: cleanUpdTSeq
Type: Package
Title: cleanUpdTSeq cleans up artifacts from polyadenylation sites from
        oligo(dT)-mediated 3' end RNA sequending data
Description: 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.
Version: 1.47.1
Date: 2025-07-22
Author: Sarah Sheppard, Haibo Liu, Jianhong Ou, Nathan Lawson, Lihua Julie Zhu
Maintainer: Jianhong Ou <jou@morgridge.org>; Lihua Julie Zhu
 <Julie.Zhu@umassmed.edu>
Depends: R (>= 3.5.0), BSgenome.Drerio.UCSC.danRer7, methods
Imports: BSgenome, GenomicRanges, seqinr, e1071, Biostrings, Seqinfo,
        IRanges, utils, stringr, stats, S4Vectors
Suggests: BiocStyle, rmarkdown, knitr, RUnit, BiocGenerics (>= 0.1.0)
License: GPL-2
biocViews: Sequencing, 3' end sequencing, polyadenylation site,
        internal priming
VignetteBuilder: knitr
RoxygenNote: 7.1.2
LazyData: true
Encoding: UTF-8
git_url: https://git.bioconductor.org/packages/cleanUpdTSeq
git_branch: devel
git_last_commit: 4f078a2
git_last_commit_date: 2025-07-22
Repository: Bioconductor 3.22
Date/Publication: 2025-07-23
NeedsCompilation: no
Packaged: 2025-07-23 22:07:53 UTC; biocbuild
Built: R 4.5.1; ; 2025-07-24 12:49:51 UTC; windows
