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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
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This package classifies putative polyadenylation sites as true or false/internally oligodT primed
Bioconductor version: Release (3.5)
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 |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GeneRegulation, Genetics, SequenceMatching, Sequencing, Software |
| Version | 1.14.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (4 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.
| Source Package | cleanUpdTSeq_1.14.0.tar.gz |
| Windows Binary | cleanUpdTSeq_1.14.0.zip |
| Mac OS X 10.11 (El Capitan) | cleanUpdTSeq_1.14.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/cleanUpdTSeq |
| Package Short Url | http://bioconductor.org/packages/cleanUpdTSeq/ |
| Package Downloads Report | Download Stats |
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