Modstrings
Working with modified nucleotide sequences
Bioconductor version: 3.24 · Package version: 1.29.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Modstrings")Details
| Maintainer | Felix G.M. Ernst <felix.gm.ernst@outlook.com> |
| Author | Felix G.M. Ernst [aut, cre] (ORCID: <https://orcid.org/0000-0001-5064-0928>), Denis L.J. Lafontaine [ctb, fnd] |
| License | Artistic-2.0 |
| Bug Reports | https://github.com/FelixErnst/Modstrings/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataImport, DataRepresentation, Infrastructure, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/Modstrings/ |
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 1.29.0, https://bioconductor.org/packages/Modstrings.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | Modstrings_1.29.0.tar.gz |
| Windows binary (x86_64) | Modstrings_1.29.0.zip |
| macOS binary (arm64) | Modstrings_1.29.0.tgz |
| macOS binary (x86_64) | Modstrings_1.29.0.tgz |
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