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: 1.50.0
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
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libxml2-dev
        libssl-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 12:37:54 UTC
RemoteUrl: https://github.com/bioc/cleanUpdTSeq
RemoteRef: RELEASE_3_23
RemoteSha: 549b1e2a5af14deb7d545927030d6eb448d8d92c
NeedsCompilation: no
Packaged: 2026-04-29 20:40:59 UTC; root
Built: R 4.6.0; ; 2026-04-29 20:46:17 UTC; windows
