XNAString
This package isdeprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.22 of Bioconductor.This package has been removed from Bioconductor.For the last stable, up-to-date release version, seeXNAString.
Efficient Manipulation of Modified Oligonucleotide Sequences
Bioconductor version: Release (3.22)
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("XNAString")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("XNAString")For older versions of R, please refer to the appropriateBioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | Alignment,Genetics,SequenceMatching,Sequencing,Software |
| Version | 1.18.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (4.5 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 |
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
FollowInstallation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| 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 |
| Package Short Url | https://bioconductor.org/packages/XNAString/ |
| Package Downloads Report | Download Stats |