cleanUpdTSeq
This is the development version of cleanUpdTSeq; for the stable release version, see cleanUpdTSeq.
cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data
Bioconductor version: Development (3.24)
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 <jou at morgridge.org>; Lihua Julie Zhu <Julie.Zhu at umassmed.edu>
citation("cleanUpdTSeq")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 1.51.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (13 years) |
| License | GPL-2 |
| Depends | R (>= 3.5.0), BSgenome.Drerio.UCSC.danRer7, methods |
| Imports | BSgenome, GenomicRanges, seqinr, e1071, Biostrings, Seqinfo, 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 | |
| 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_1.51.0.tar.gz |
| Windows Binary (x86_64) | cleanUpdTSeq_1.51.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | cleanUpdTSeq_1.51.0.tgz |
| macOS Binary (sonoma-arm64) | cleanUpdTSeq_1.51.0.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 |