cleanUpdTSeq

This package is for version 3.8 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: 3.8

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: 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 "3.5") and enter:


if (!require("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")

cleanUpdTSeq Vignette HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneRegulation, Genetics, SequenceMatching, Sequencing, Software

Version 1.20.1

In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)

License GPL-2

Depends R (>= 2.15), BiocGenerics(>= 0.1.0), methods, BSgenome, BSgenome.Drerio.UCSC.danRer7, GenomicRanges, seqinr, e1071

Imports

System Requirements

URL

Suggests BiocStyle, knitr, RUnit

Linking To

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Depends On Me

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Build Report Build Report

Package Archives

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

Source Package cleanUpdTSeq_1.20.1.tar.gz

Windows Binary cleanUpdTSeq_1.20.1.zip

Mac OS X 10.11 (El Capitan) cleanUpdTSeq_1.20.1.tgz

Source Repository git clone https://git.bioconductor.org/packages/cleanUpdTSeq

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cleanUpdTSeq

Bioc Package Browser https://code.bioconductor.org/browse/cleanUpdTSeq/

Package Short Url https://bioconductor.org/packages/cleanUpdTSeq/

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Old Source Packages for BioC 3.8 Source Archive