To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("cleanUpdTSeq")

In most cases, you don't need to download the package archive at all.

cleanUpdTSeq

 

   

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

Bioconductor version: Release (3.4)

This package uses the Naive Bayes classifier (from e1071) to assign probability values to putative polyadenylation sites (pA sites) based on training data from zebrafish. This will allow the user to separate true, biologically relevant pA sites from false, oligodT primed pA sites.

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

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

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("cleanUpdTSeq")

Documentation

HTML R Script cleanUpdTSeq Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneRegulation, Genetics, SequenceMatching, Sequencing, Software
Version 1.12.0
In Bioconductor since BioC 2.13 (R-3.0) (3.5 years)
License GPL-2
Depends R (>= 2.15), BiocGenerics(>= 0.1.0), methods, BSgenome, BSgenome.Drerio.UCSC.danRer7, GenomicRanges, seqinr, e1071
Imports
LinkingTo
Suggests BiocStyle, knitr, RUnit
SystemRequirements
Enhances
URL
Depends On Me
Imports Me InPAS
Suggests Me
Build Report  

Package Archives

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

Package Source cleanUpdTSeq_1.12.0.tar.gz
Windows Binary cleanUpdTSeq_1.12.0.zip
Mac OS X 10.9 (Mavericks) cleanUpdTSeq_1.12.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/cleanUpdTSeq/tree/release-3.4
Package Short Url http://bioconductor.org/packages/cleanUpdTSeq/
Package Downloads Report Download Stats

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