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Modstrings

Working with modified nucleotide sequences


Bioconductor version: Release (3.18)

Representing nucleotide modifications in a nucleotide sequence is usually done via special characters from a number of sources. This represents a challenge to work with in R and the Biostrings package. The Modstrings package implements this functionallity for RNA and DNA sequences containing modified nucleotides by translating the character internally in order to work with the infrastructure of the Biostrings package. For this the ModRNAString and ModDNAString classes and derivates and functions to construct and modify these objects despite the encoding issues are implemenented. In addition the conversion from sequences to list like location information (and the reverse operation) is implemented as well.

Author: Felix G.M. Ernst [aut, cre] , Denis L.J. Lafontaine [ctb, fnd]

Maintainer: Felix G.M. Ernst <felix.gm.ernst at outlook.com>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Modstrings")

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("Modstrings")
Modstrings HTML R Script
Modstrings-DNA-alphabet HTML R Script
Modstrings-RNA-alphabet HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataImport, DataRepresentation, Infrastructure, Sequencing, Software
Version 1.18.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License Artistic-2.0
Depends R (>= 3.6), Biostrings(>= 2.51.5)
Imports methods, BiocGenerics, GenomicRanges, S4Vectors, IRanges, XVector, stringi, stringr, crayon, grDevices
System Requirements
URL
Bug Reports https://github.com/FelixErnst/Modstrings/issues
See More
Suggests BiocStyle, knitr, rmarkdown, testthat, usethis
Linking To
Enhances
Depends On Me EpiTxDb, RNAmodR, tRNAdbImport
Imports Me tRNA
Suggests Me EpiTxDb.Hs.hg38, EpiTxDb.Sc.sacCer3
Links To Me
Build Report Build Report

Package Archives

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

Source Package Modstrings_1.18.0.tar.gz
Windows Binary Modstrings_1.18.0.zip
macOS Binary (x86_64) Modstrings_1.18.0.tgz
macOS Binary (arm64) Modstrings_1.18.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/Modstrings
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Modstrings
Bioc Package Browser https://code.bioconductor.org/browse/Modstrings/
Package Short Url https://bioconductor.org/packages/Modstrings/
Package Downloads Report Download Stats