Structstrings
This is the development version of Structstrings; for the stable release version, see Structstrings.
Implementation of the dot bracket annotations with Biostrings
Bioconductor version: Development (3.24)
The Structstrings package implements the widely used dot bracket annotation for storing base pairing information in structured RNA. Structstrings uses the infrastructure provided by the Biostrings package and derives the DotBracketString and related classes from the BString class. From these, base pair tables can be produced for in depth analysis. In addition, the loop indices of the base pairs can be retrieved as well. For better efficiency, information conversion is implemented in C, inspired to a large extend by the ViennaRNA package.
Author: Felix G.M. Ernst [aut, cre]
Maintainer: Felix G.M. Ernst <felix.gm.ernst at outlook.com>
citation("Structstrings")):
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("Structstrings")
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("Structstrings")| Structstrings | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, DataImport, DataRepresentation, Infrastructure, SequenceMatching, Sequencing, Software |
| Version | 1.29.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.0), S4Vectors(>= 0.47.2), IRanges(>= 2.23.9), Biostrings(>= 2.57.2) |
| Imports | methods, BiocGenerics, XVector, stringr, stringi, crayon, grDevices |
| System Requirements | |
| URL | https://github.com/FelixErnst/Structstrings |
| Bug Reports | https://github.com/FelixErnst/Structstrings/issues |
See More
| Suggests | testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle |
| Linking To | IRanges, S4Vectors |
| Enhances | |
| Depends On Me | tRNA, tRNAdbImport |
| Imports Me | tRNAscanImport |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Structstrings_1.29.0.tar.gz |
| Windows Binary (x86_64) | Structstrings_1.29.0.zip |
| macOS Binary (big-sur-x86_64) | Structstrings_1.29.0.tgz |
| macOS Binary (sonoma-arm64) | Structstrings_1.29.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Structstrings |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Structstrings |
| Bioc Package Browser | https://code.bioconductor.org/browse/Structstrings/ |
| Package Short Url | https://bioconductor.org/packages/Structstrings/ |
| Package Downloads Report | Download Stats |