cleanUpdTSeq
cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data
Bioconductor version: 3.23 · Package version: 1.50.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("cleanUpdTSeq")Details
| Maintainer | Jianhong Ou <jou@morgridge.org>; Lihua Julie Zhu <Julie.Zhu@umassmed.edu> |
| Author | Sarah Sheppard, Haibo Liu, Jianhong Ou, Nathan Lawson, Lihua Julie Zhu |
| License | GPL-2 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | 3' end sequencing, Sequencing, Software, internal priming, polyadenylation site |
| Package Short Url | https://bioconductor.org/packages/cleanUpdTSeq/ |
Citation
From within R, enter citation("cleanUpdTSeq"):
Sarah Sheppard, Haibo Liu, Jianhong Ou, Nathan Lawson, Lihua Julie Zhu. cleanUpdTSeq: cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data. doi:10.18129/B9.bioc.cleanUpdTSeq, R package version 1.50.0, https://bioconductor.org/packages/cleanUpdTSeq.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | cleanUpdTSeq_1.50.0.tar.gz |
| Windows binary (x86_64) | cleanUpdTSeq_1.50.0.zip |
| macOS binary (arm64) | cleanUpdTSeq_1.50.0.tgz |
| macOS binary (x86_64) | cleanUpdTSeq_1.50.0.tgz |
Dependencies
Depends: R (>= 3.5.0), BSgenome.Drerio.UCSC.danRer7, methods
Imports: BSgenome, GenomicRanges, seqinr, e1071, Biostrings, Seqinfo, IRanges, utils, stringr, stats, S4Vectors
Suggests: BiocStyle, rmarkdown, knitr, RUnit, BiocGenerics (>= 0.1.0)
Reverse dependencies
Imports Me (1): InPAS