cleanUpdTSeq

DOI: 10.18129/B9.bioc.cleanUpdTSeq    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see cleanUpdTSeq.

This package classifies putative polyadenylation sites as true or false/internally oligodT primed

Bioconductor version: 3.12

This package implements a Naive Bayes classifier for accurate identification of polyadenylation sites (pA sites) from oligodT based 3 prime end sequencing such as PAS-Seq, PolyA-Seq and RNA-Seq. The classifer is highly accurate and outperforms heuristic methods.

Author: Sarah Sheppard, Jianhong Ou, Nathan Lawson, Lihua Julie Zhu

Maintainer: Jianhong Ou <Jianhong.Ou at duke.edu>; Lihua Julie Zhu <Julie.Zhu at umassmed.edu>

Installation

To install this package, start R (version "4.0") 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	GeneRegulation, Genetics, SequenceMatching, Sequencing, Software
Version	1.28.0
In Bioconductor since	BioC 2.13 (R-3.0) (7.5 years)
License	GPL-2
Depends	R (>= 3.5.0), BiocGenerics(>= 0.1.0), methods, stats
Imports	BSgenome, GenomicRanges, seqinr, e1071, GenomeInfoDb, IRanges, utils, BSgenome.Drerio.UCSC.danRer7
LinkingTo
Suggests	BiocStyle, knitr, RUnit
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_1.28.0.tar.gz
Windows Binary	cleanUpdTSeq_1.28.0.zip
macOS 10.13 (High Sierra)	cleanUpdTSeq_1.28.0.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/
Package Downloads Report	Download Stats