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cleanUpdTSeq

This is the development version of cleanUpdTSeq; for the stable release version, see cleanUpdTSeq.

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


Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews 3' end sequencing, Sequencing, Software, internal priming, polyadenylation site
Version 1.41.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 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, S4Vectors
System Requirements
URL
See More
Suggests BiocStyle, rmarkdown, knitr, RUnit, BiocGenerics(>= 0.1.0)
Linking To
Enhances
Depends On Me
Imports Me InPAS
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package cleanUpdTSeq_1.41.0.tar.gz
Windows Binary cleanUpdTSeq_1.41.0.zip (64-bit only)
macOS Binary (x86_64) cleanUpdTSeq_1.41.0.tgz
macOS Binary (arm64) cleanUpdTSeq_1.41.0.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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