XNAString
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see XNAString.
Efficient Manipulation of Modified Oligonucleotide Sequences
Bioconductor version: 3.14
The XNAString package allows for description of base sequences and associated chemical modifications in a single object. XNAString is able to capture single stranded, as well as double stranded molecules. Chemical modifications are represented as independent strings associated with different features of the molecules (base sequence, sugar sequence, backbone sequence, modifications) and can be read or written to a HELM notation. It also enables secondary structure prediction using RNAfold from ViennaRNA (distributed under its own \licence{https://github.com/ViennaRNA/ViennaRNA/blob/master/license.txt}; \citation{https://github.com/plucinskam/XNAString/blob/master/README.md#dependencies}). XNAString is designed to be efficient representation of nucleic-acid based therapeutics, therefore it stores information about target sequences and provides interface for matching and alignment functions from Biostrings package.
Author: Anna Górska [aut], Marianna Plucinska [aut, cre], Lykke Pedersen [aut], Lukasz Kielpinski [aut], Disa Tehler [aut], Peter H. Hagedorn [aut]
Maintainer: Marianna Plucinska <marianna.plucinska at roche.com>
citation("XNAString")):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("XNAString")
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("XNAString")| XNAString_vignette | HTML | R Script |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | Alignment, Genetics, SequenceMatching, Sequencing, Software |
| Version | 1.2.2 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3 years) |
| License | GPL-2 |
| Depends | R (>= 4.1) |
| Imports | utils, Biostrings, BSgenome, data.table, GenomicRanges, IRanges, methods, Rcpp, stringi, S4Vectors, future.apply, stringr, formattable, stats |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, rmarkdown, markdown, testthat, BSgenome.Hsapiens.UCSC.hg38, pander |
| Linking To | Rcpp |
| 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 | XNAString_1.2.2.tar.gz |
| Windows Binary | XNAString_1.2.2.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | XNAString_1.2.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/XNAString |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/XNAString |
| Bioc Package Browser | https://code.bioconductor.org/browse/XNAString/ |
| Package Short Url | https://bioconductor.org/packages/XNAString/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.14 | Source Archive |