cleanUpdTSeq
This package is for version 3.9 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: 3.9
This package implements a Naive Bayes classifier for accurate identification of polyadenylation sites (pA sites) from oligodT based 3 prime end sequencing such as PAS-Seq, PolyA-Seq and RNA-Seq. The classifer is highly accurate and outperforms heuristic methods.
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 "3.6") 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 | 1.22.2 |
| In Bioconductor since | BioC 2.13 (R-3.0) (10.5 years) |
| License | GPL-2 |
| Depends | R (>= 2.15), BiocGenerics(>= 0.1.0), methods, stats |
| Imports | BSgenome, GenomicRanges, seqinr, e1071, GenomeInfoDb, IRanges, utils, BSgenome.Drerio.UCSC.danRer7 |
| 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_1.22.2.tar.gz |
| Windows Binary | cleanUpdTSeq_1.22.2.zip |
| Mac OS X 10.11 (El Capitan) | cleanUpdTSeq_1.22.2.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/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |