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("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 | ||
| NEWS | Text |
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 |
See More
| Suggests | BiocStyle, knitr, RUnit |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | InPAS |
| Suggests Me | |
| Links To Me | |
| 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 [email protected]:packages/cleanUpdTSeq |
| Bioc Package Browser | https://code.bioconductor.org/browse/cleanUpdTSeq/ |
| Package Short Url | https://bioconductor.org/packages/cleanUpdTSeq/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.8 | Source Archive |