Modstrings

DOI: 10.18129/B9.bioc.Modstrings    

Working with modified nucleotide sequences

Bioconductor version: Release (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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	DataImport, DataRepresentation, Infrastructure, Sequencing, Software
Version	1.8.0
In Bioconductor since	BioC 3.9 (R-3.6) (2.5 years)
License	Artistic-2.0
Depends	R (>= 3.6), Biostrings(>= 2.51.5)
Imports	methods, BiocGenerics, GenomicRanges, S4Vectors, IRanges, XVector, stringi, stringr, crayon, grDevices
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat, usethis
SystemRequirements
Enhances
URL
BugReports	https://github.com/FelixErnst/Modstrings/issues
Depends On Me	EpiTxDb, RNAmodR, tRNAdbImport
Imports Me	tRNA
Suggests Me	EpiTxDb.Hs.hg38, EpiTxDb.Sc.sacCer3
Links To Me
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
Package Short Url	https://bioconductor.org/packages/Modstrings/
Package Downloads Report	Download Stats