R4RNA
This is the development version of R4RNA; for the stable release version, see R4RNA.
An R package for RNA visualization and analysis
Bioconductor version: Development (3.24)
A package for RNA basepair analysis, including the visualization of basepairs as arc diagrams for easy comparison and annotation of sequence and structure. Arc diagrams can additionally be projected onto multiple sequence alignments to assess basepair conservation and covariation, with numerical methods for computing statistics for each.
Author: Daniel Lai, Irmtraud Meyer <irmtraud.meyer at cantab.net>
Maintainer: Daniel Lai <jujubix at cs.ubc.ca>
citation("R4RNA")):
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("R4RNA")
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("R4RNA")| R4RNA.pdf | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, DataImport, DataRepresentation, MultipleComparison, MultipleSequenceAlignment, Preprocessing, Software, Visualization |
| Version | 1.41.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.2.0), Biostrings(>= 2.38.0) |
| Imports | |
| System Requirements | |
| URL | http://www.e-rna.org/r-chie/ |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | ggmsa, rnaCrosslinkOO |
| Suggests Me | rfaRm |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | R4RNA_1.41.0.tar.gz |
| Windows Binary (x86_64) | R4RNA_1.41.0.zip |
| macOS Binary (big-sur-x86_64) | R4RNA_1.41.0.tgz |
| macOS Binary (sonoma-arm64) | R4RNA_1.41.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/R4RNA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/R4RNA |
| Bioc Package Browser | https://code.bioconductor.org/browse/R4RNA/ |
| Package Short Url | https://bioconductor.org/packages/R4RNA/ |
| Package Downloads Report | Download Stats |