cleanUpdTSeq

DOI: 10.18129/B9.bioc.cleanUpdTSeq    

This package is for version 3.7 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: 3.7

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

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 1.18.0
In Bioconductor since BioC 2.13 (R-3.0) (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
Links To Me
Build Report  

Package Archives

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

Source Package cleanUpdTSeq_1.18.0.tar.gz
Windows Binary cleanUpdTSeq_1.18.0.zip
Mac OS X 10.11 (El Capitan) cleanUpdTSeq_1.18.0.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 http://bioconductor.org/packages/cleanUpdTSeq/
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