DOI: 10.18129/B9.bioc.cleanUpdTSeq    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see cleanUpdTSeq.

This package classifies putative polyadenylation sites as true or false/internally oligodT primed

Bioconductor version: 3.10

This package implements a Naive Bayes classifier for accurate identification of polyadenylation sites (pA sites) from oligodT based 3 prime end sequencing such as PAS-Seq, PolyA-Seq and RNA-Seq. The classifer is highly accurate and outperforms heuristic methods.

Author: Sarah Sheppard, 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")):


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biocViews GeneRegulation, Genetics, SequenceMatching, Sequencing, Software
Version 1.24.0
In Bioconductor since BioC 2.13 (R-3.0) (6.5 years)
License GPL-2
Depends R (>= 2.15), BiocGenerics(>= 0.1.0), methods, stats
Imports BSgenome, GenomicRanges, seqinr, e1071, GenomeInfoDb, IRanges, utils, BSgenome.Drerio.UCSC.danRer7
Suggests BiocStyle, knitr, RUnit
Depends On Me
Imports Me InPAS
Suggests Me
Links To Me
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