haibol2016/cleanUpdTSeq: cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data

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.

Getting started

Package details

AuthorSarah Sheppard, Haibo Liu, Jianhong Ou, Nathan Lawson, Lihua Julie Zhu
Bioconductor views 3' end sequencing Sequencing internal priming polyadenylation site
MaintainerJianhong Ou <Jianhong.Ou@duke.edu>; Lihua Julie Zhu <Julie.Zhu@umassmed.edu>
LicenseGPL-2
Version1.33.1
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("remotes")
remotes::install_github("haibol2016/cleanUpdTSeq")
haibol2016/cleanUpdTSeq documentation built on April 14, 2022, 9:56 p.m.