DOI: 10.18129/B9.bioc.cleanUpdTSeq  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see cleanUpdTSeq.

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

Bioconductor version: 3.16

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>

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biocViews 3' end sequencing, Sequencing, Software, internal priming, polyadenylation site
Version 1.36.0
In Bioconductor since BioC 2.13 (R-3.0) (9.5 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
Suggests BiocStyle, rmarkdown, knitr, RUnit, BiocGenerics(>= 0.1.0)
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