Modstrings
This is the released version of Modstrings; for the devel version, see Modstrings.
All Bioconductor versions of Modstrings
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9
Working with modified nucleotide sequences
Bioconductor version: 3.23 · Package version: 1.28.0
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"):
Felix G.M. Ernst. Modstrings: Working with modified nucleotide sequences. doi:10.18129/B9.bioc.Modstrings, R package version 1.28.0, https://bioconductor.org/packages/Modstrings.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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.
Details
| Version | 1.28.0 |
| License | Artistic-2.0 |
| Bug Reports | https://github.com/FelixErnst/Modstrings/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7 years) |
| Downloads rank | 1011 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataImport, DataRepresentation, Infrastructure, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/Modstrings/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("Modstrings")| Modstrings | HTML | R Script |
| ModDNAString alphabet | HTML | R Script |
| ModRNAString alphabet | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | Modstrings_1.28.0.tar.gz |
| Windows binary (x86_64) | Modstrings_1.28.0.zip |
| macOS binary (arm64) | Modstrings_1.28.0.tgz |
| macOS binary (x86_64) | Modstrings_1.28.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Modstrings |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Modstrings |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 3.6), Biostrings (>= 2.79.3)
Imports: methods, BiocGenerics, GenomicRanges, S4Vectors, IRanges, XVector, stringi, stringr, crayon, grDevices
Reverse dependencies
Depends On Me (3): EpiTxDb, RNAmodR, tRNAdbImport
Imports Me (1): tRNA
Suggests Me (2): EpiTxDb.Hs.hg38, EpiTxDb.Sc.sacCer3