cleanUpdTSeq

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

Bioconductor version: Release (2.14)

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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("cleanUpdTSeq")

Documentation

PDF R Script cleanUpdTSeq Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneRegulation, Genetics, SequenceMatching, Sequencing, Software
Version 1.2.0
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
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Package Downloads

Package Source cleanUpdTSeq_1.2.0.tar.gz
Windows Binary cleanUpdTSeq_1.2.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) cleanUpdTSeq_1.2.0.tgz
Mac OS X 10.9 (Mavericks)
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