Registration Open for Bioc2024 July 24-26


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 (3.20)

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.


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 1.43.0
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
System Requirements
See More
Suggests BiocStyle, rmarkdown, knitr, RUnit, BiocGenerics(>= 0.1.0)
Linking To
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package cleanUpdTSeq_1.43.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) cleanUpdTSeq_1.43.0.tgz
macOS Binary (arm64) cleanUpdTSeq_1.43.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats