This is the released version of cleanUpdTSeq; for the devel version, see cleanUpdTSeq.
cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending dataBioconductor version: Release (3.21)
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 <jou at morgridge.org>; Lihua Julie Zhu <Julie.Zhu at umassmed.edu>
Citation (from within R, entercitation("cleanUpdTSeq")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("cleanUpdTSeq")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("cleanUpdTSeq")Follow Installation instructions to use this package in your R session.
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