source("http://bioconductor.org/biocLite.R")
biocLite("cleanUpdTSeq")

cleanUpdTSeq

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

Bioconductor version: 2.13

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>

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("cleanUpdTSeq")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("cleanUpdTSeq")

 

PDF	R Script	cleanUpdTSeq Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneRegulation, Genetics, HighThroughputSequencing, SequenceMatching, Software
Version	1.0.2
In Bioconductor since	BioC 2.13 (R-3.0)
License	GPL-2
Depends	R (>= 2.15), BiocGenerics(>= 0.1.0), BSgenome, BSgenome.Drerio.UCSC.danRer7, GenomicRanges, seqinr, e1071
Imports
Suggests
System Requirements
URL
Depends On Me
Imports Me
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Package Archives

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

Package Source	cleanUpdTSeq_1.0.2.tar.gz
Windows Binary	cleanUpdTSeq_1.0.2.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	cleanUpdTSeq_1.0.2.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats