cleanUpdTSeq

DOI: 10.18129/B9.bioc.cleanUpdTSeq    

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

Bioconductor version: Release (3.10)

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>

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

Installation

To install this package, start R (version "3.6") 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 1.24.0
In Bioconductor since BioC 2.13 (R-3.0) (6 years)
License GPL-2
Depends R (>= 2.15), 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_1.24.0.tar.gz
Windows Binary cleanUpdTSeq_1.24.0.zip
Mac OS X 10.11 (El Capitan) cleanUpdTSeq_1.24.0.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

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