Modstrings
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see Modstrings.
Working with modified nucleotide sequences
Bioconductor version: 3.13
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("Modstrings")):
Installation
To install this package, start R (version "4.1") 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 | ||
| NEWS | Text |
Details
| biocViews | DataImport, DataRepresentation, Infrastructure, Sequencing, Software |
| Version | 1.8.0 |
| 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_1.8.0.tar.gz |
| Windows Binary | Modstrings_1.8.0.zip |
| macOS 10.13 (High Sierra) | Modstrings_1.8.0.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 |
| Old Source Packages for BioC 3.13 | Source Archive |