cleanUpdTSeq
This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see cleanUpdTSeq.
cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data
Bioconductor version: 3.18
This package implements a Naive Bayes classifier for accurately differentiating true polyadenylation sites (pA sites) from oligo(dT)-mediated 3' end sequencing such as PAS-Seq, PolyA-Seq and RNA-Seq by filtering out false polyadenylation sites, mainly due to oligo(dT)-mediated internal priming during reverse transcription. The classifer is highly accurate and outperforms other heuristic methods.
Author: Sarah Sheppard, Haibo Liu, 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 "4.3") 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 | 3' end sequencing, Sequencing, Software, internal priming, polyadenylation site |
| Version | 1.40.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (10.5 years) |
| License | GPL-2 |
| Depends | R (>= 3.5.0), BSgenome.Drerio.UCSC.danRer7, methods |
| Imports | BSgenome, GenomicRanges, seqinr, e1071, Biostrings, GenomeInfoDb, IRanges, utils, stringr, stats, S4Vectors |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, rmarkdown, knitr, RUnit, BiocGenerics(>= 0.1.0) |
| 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_1.40.0.tar.gz |
| Windows Binary | cleanUpdTSeq_1.40.0.zip (64-bit only) |
| macOS Binary (x86_64) | cleanUpdTSeq_1.40.0.tgz |
| macOS Binary (arm64) | cleanUpdTSeq_1.40.0.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 |