Bioconductor version: Release (3.11)
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 (from within R,
enter citation("cleanUpdTSeq")
):
To install this package, start R (version "4.0") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("cleanUpdTSeq")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("cleanUpdTSeq")
HTML | R Script | cleanUpdTSeq Vignette |
Reference Manual | ||
Text | NEWS |
biocViews | GeneRegulation, Genetics, SequenceMatching, Sequencing, Software |
Version | 1.26.0 |
In Bioconductor since | BioC 2.13 (R-3.0) (7 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 |
LinkingTo | |
Suggests | BiocStyle, knitr, RUnit |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | InPAS |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | cleanUpdTSeq_1.26.0.tar.gz |
Windows Binary | cleanUpdTSeq_1.26.0.zip |
macOS 10.13 (High Sierra) | cleanUpdTSeq_1.26.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/cleanUpdTSeq |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/cleanUpdTSeq |
Package Short Url | https://bioconductor.org/packages/cleanUpdTSeq/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.11 | Source Archive |
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