XNAString

Efficient Manipulation of Modified Oligonucleotide Sequences

Bioconductor version: Release (3.19)

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. 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 and pwalign packages.

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 (from within R, enter citation("XNAString")):

Installation

To install this package, start R (version "4.4") 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 classes and functionalities	HTML	R Script
Reference Manual	PDF
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, Genetics, SequenceMatching, Sequencing, Software
Version	1.12.0
In Bioconductor since	BioC 3.13 (R-4.1) (3.5 years)
License	GPL-2
Depends	R (>= 4.1)
Imports	utils, Biostrings, pwalign, BSgenome, data.table, GenomicRanges, IRanges, methods, Rcpp, stringi, S4Vectors, future.apply, stringr, formattable, stats
System Requirements
URL

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_1.12.0.tar.gz
Windows Binary (x86_64)	XNAString_1.12.0.zip
macOS Binary (x86_64)	XNAString_1.12.0.tgz
macOS Binary (arm64)	XNAString_1.12.0.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