RNAmodR.RiboMethSeq
This is the development version of RNAmodR.RiboMethSeq; for the stable release version, see RNAmodR.RiboMethSeq.
Detection of 2'-O methylations by RiboMethSeq
Bioconductor version: Development (3.24)
RNAmodR.RiboMethSeq implements the detection of 2'-O methylations on RNA from experimental data generated with the RiboMethSeq protocol. The package builds on the core functionality of the RNAmodR package to detect specific patterns of the modifications in high throughput sequencing data.
Author: Felix G.M. Ernst [aut, cre]
, Denis L.J. Lafontaine [ctb, fnd]
Maintainer: Felix G.M. Ernst <felix.gm.ernst at outlook.com>
citation("RNAmodR.RiboMethSeq")):
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("RNAmodR.RiboMethSeq")
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("RNAmodR.RiboMethSeq")| RNAmodR.RiboMethSeq | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Sequencing, Software, Visualization, WorkflowStep |
| Version | 1.27.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.0), RNAmodR(>= 1.5.3) |
| Imports | methods, S4Vectors, BiocGenerics, IRanges, GenomicRanges, Gviz |
| System Requirements | |
| URL | https://github.com/FelixErnst/RNAmodR.RiboMethSeq |
| Bug Reports | https://github.com/FelixErnst/RNAmodR.RiboMethSeq/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat, rtracklayer, Seqinfo, RNAmodR.Data |
| 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 | RNAmodR.RiboMethSeq_1.27.0.tar.gz |
| Windows Binary (x86_64) | RNAmodR.RiboMethSeq_1.27.0.zip |
| macOS Binary (big-sur-x86_64) | RNAmodR.RiboMethSeq_1.27.0.tgz |
| macOS Binary (sonoma-arm64) | RNAmodR.RiboMethSeq_1.27.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/RNAmodR.RiboMethSeq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/RNAmodR.RiboMethSeq |
| Bioc Package Browser | https://code.bioconductor.org/browse/RNAmodR.RiboMethSeq/ |
| Package Short Url | https://bioconductor.org/packages/RNAmodR.RiboMethSeq/ |
| Package Downloads Report | Download Stats |