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XNAString

This is the development version of XNAString; for the stable release version, see XNAString.

Efficient Manipulation of Modified Oligonucleotide Sequences


Bioconductor version: Development (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 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 (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Alignment, Genetics, SequenceMatching, Sequencing, Software
Version 1.11.0
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
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package XNAString_1.11.0.tar.gz
Windows Binary
macOS Binary (x86_64) XNAString_1.11.0.tgz
macOS Binary (arm64)
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