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This is the development version of cleanUpdTSeq; for the stable release version, see cleanUpdTSeq.

cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data

Bioconductor version: Development (3.19)

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.

Author: Sarah Sheppard, Haibo Liu, Jianhong Ou, Nathan Lawson, Lihua Julie Zhu

Maintainer: Jianhong Ou <Jianhong.Ou at>; Lihua Julie Zhu <Julie.Zhu at>

Citation (from within R, enter citation("cleanUpdTSeq")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


Reference Manual PDF


biocViews 3' end sequencing, Sequencing, Software, internal priming, polyadenylation site
Version 1.41.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)
License GPL-2
Depends R (>= 3.5.0), BSgenome.Drerio.UCSC.danRer7, methods
Imports BSgenome, GenomicRanges, seqinr, e1071, Biostrings, GenomeInfoDb, IRanges, utils, stringr, stats, S4Vectors
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Suggests BiocStyle, rmarkdown, knitr, RUnit, BiocGenerics(>= 0.1.0)
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