cleanUpdTSeq

DOI: 10.18129/B9.bioc.cleanUpdTSeq    

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

Bioconductor version: Release (3.13)

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 duke.edu>; Lihua Julie Zhu <Julie.Zhu at umassmed.edu>

Citation (from within R, enter citation("cleanUpdTSeq")):

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("cleanUpdTSeq")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("cleanUpdTSeq")

 

HTML R Script cleanUpdTSeq Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews 3' end sequencing, Sequencing, Software, internal priming, polyadenylation site
Version 1.30.0
In Bioconductor since BioC 2.13 (R-3.0) (7.5 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
LinkingTo
Suggests BiocStyle, rmarkdown, knitr, RUnit, BiocGenerics(>= 0.1.0)
SystemRequirements
Enhances
URL
Depends On Me
Imports Me InPAS
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package cleanUpdTSeq_1.30.0.tar.gz
Windows Binary cleanUpdTSeq_1.30.0.zip
macOS 10.13 (High Sierra) cleanUpdTSeq_1.30.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/cleanUpdTSeq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cleanUpdTSeq
Package Short Url https://bioconductor.org/packages/cleanUpdTSeq/
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