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

Bioconductor version: Release (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))


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


To view documentation for the version of this package installed in your system, start R and enter:

cleanUpdTSeq Vignette HTML R Script
Reference Manual PDF


biocViews 3' end sequencing, Sequencing, Software, internal priming, polyadenylation site
Version 1.42.0
In Bioconductor since BioC 2.13 (R-3.0) (11 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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Follow Installation instructions to use this package in your R session.

Source Package cleanUpdTSeq_1.42.0.tar.gz
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macOS Binary (x86_64) cleanUpdTSeq_1.42.0.tgz
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