cleanUpdTSeq

DOI:10.18129/B9.bioc.cleanUpdTSeq

This is thedevelopmentversion of cleanUpdTSeq; for the stable release version, seecleanUpdTSeq.

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

Bioconductor version: Development (3.17)

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 ; Lihua Julie Zhu

Installation

To install this package, start R (version "4.3") 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 appropriateBioconductor release.

Documentation

查看文档的版本包age 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	1.37.0
In Bioconductor since	BioC 2.13 (R-3.0) (9.5 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
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

Followbob 体育网址 instructions to use this package in your R session.

Source Package	cleanUpdTSeq_1.37.0.tar.gz
Windows Binary	cleanUpdTSeq_1.37.0.zip(64-bit only)
macOS Binary (x86_64)	cleanUpdTSeq_1.37.0.tgz
macOS Binary (arm64)	cleanUpdTSeq_1.37.0.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	//www.anjoumacpherson.com/packages/cleanUpdTSeq/
Package Downloads Report	Download Stats