XNAString

DOI: 10.18129/B9.bioc.XNAString    

Efficient Manipulation of Modified Oligonucleotide Sequences

Bioconductor version: Release (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>

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")

 

HTML	R Script	XNAString_vignette
PDF		Reference Manual
Text		LICENSE

Details

biocViews	Alignment, Genetics, SequenceMatching, Sequencing, Software
Version	1.2.2
In Bioconductor since	BioC 3.13 (R-4.1) (1 year)
License	GPL-2
Depends	R (>= 4.1)
Imports	utils, Biostrings, BSgenome, data.table, GenomicRanges, IRanges, methods, Rcpp, stringi, S4Vectors, future.apply, stringr, formattable, stats
LinkingTo	Rcpp
Suggests	BiocStyle, knitr, rmarkdown, markdown, testthat, BSgenome.Hsapiens.UCSC.hg38, pander
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
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
Package Short Url	https://bioconductor.org/packages/XNAString/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive