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

Efficient Manipulation of Modified Oligonucleotide Sequences

Bioconductor version: Development (3.20)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

XNAString classes and functionalities HTML R Script
Reference Manual PDF


biocViews Alignment, Genetics, SequenceMatching, Sequencing, Software
Version 1.13.0
In Bioconductor since BioC 3.13 (R-4.1) (3 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
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Suggests BiocStyle, knitr, rmarkdown, markdown, testthat, BSgenome.Hsapiens.UCSC.hg38, pander
Linking To Rcpp
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Follow Installation instructions to use this package in your R session.

Source Package XNAString_1.13.0.tar.gz
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macOS Binary (x86_64) XNAString_1.13.0.tgz
macOS Binary (arm64) XNAString_1.13.0.tgz
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Source Repository (Developer Access) git clone
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