cleanUpdTSeq

This package is for version 3.19 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: 3.19

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 "4.4") 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.

Documentation

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

browseVignettes("cleanUpdTSeq")

cleanUpdTSeq Vignette HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews 3' end sequencing, Sequencing, Software, internal priming, polyadenylation site

Version 1.42.0

In Bioconductor since BioC 2.13 (R-3.0) (11 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

System Requirements

URL

Suggests BiocStyle, rmarkdown, knitr, RUnit, BiocGenerics(>= 0.1.0)

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Package Archives

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

Source Package cleanUpdTSeq_1.42.0.tar.gz

Windows Binary (x86_64) cleanUpdTSeq_1.42.0.zip

macOS Binary (x86_64) cleanUpdTSeq_1.42.0.tgz

macOS Binary (arm64) cleanUpdTSeq_1.42.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/cleanUpdTSeq

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cleanUpdTSeq

Bioc Package Browser https://code.bioconductor.org/browse/cleanUpdTSeq/

Package Short Url https://bioconductor.org/packages/cleanUpdTSeq/

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