https://github.com/bioconductor-source/xnastring
Science Score: 26.0%
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Repository
Basic Info
- Host: GitHub
- Owner: bioconductor-source
- License: gpl-2.0
- Language: C
- Default Branch: devel
- Size: 1.63 MB
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- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
XNAString: Efficient manipulation of modified oligonucleotide sequences
Description
The XNAString package allows for description of base sequences and associated chemical modifications in a single object. XNAString is able to capture single stranded, as well as double stranded molecules. Chemical modifications are represented as independent strings associated with different features of the molecules (base sequence, sugar sequence, backbone sequence, modifications) and can be read or written to a HELM notation. It also enables secondary structure prediction using RNAfold from ViennaRNA. XNAString is designed to be efficient representation of nucleic-acid based therapeutics, therefore it stores information about target sequences and provides interface for matching and alignment functions from Biostrings package.
Usage
See vignette for usage examples
Dependencies
1) Biostrings - Matching & alignment methods (matchPattern, vmatchPattern, pairwiseAlignment and matchPDict) are inherited from Biostrings R package. Check Biostrings repository for detailed information.
2) ViennaRNA - Source code of ViennaRNA is included in XNAString package and used for secondary structure prediction. Please note that ViennaRNA is distributed under its own licence.
Citation:
* Lorenz, R., Bernhart, S.H., Höner zu Siederdissen, C. et al. ViennaRNA Package 2.0. Algorithms Mol Biol 6, 26 (2011). https://doi.org/10.1186/1748-7188-6-26
* Hofacker, I.L., Fontana, W., Stadler, P.F. et al. Fast folding and comparison of RNA secondary structures. Monatsh Chem 125, 167–188 (1994). https://doi.org/10.1007/BF0081816
Authors
Lykke Pedersen (1)
Łukasz J. Kiełpiński (1)
Anna Górska (2)
Marianna Plucinska (2)
Disa Tehler (1)
Peter H. Hagedorn (1)
(1) Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, DK-2970 Hørsholm, Denmark.
(2) Roche Global IT Solution Centre, Roche Polska Sp. z o.o.
Owner
- Name: (WIP DEV) Bioconductor Packages
- Login: bioconductor-source
- Kind: organization
- Email: maintainer@bioconductor.org
- Website: https://bioconductor.org
- Repositories: 1
- Profile: https://github.com/bioconductor-source
Source code for packages accepted into Bioconductor
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Dependencies
- actions/cache v2 composite
- actions/checkout v2 composite
- actions/upload-artifact master composite
- r-lib/actions/setup-pandoc master composite
- r-lib/actions/setup-r master composite
- R >= 4.1 depends
- BSgenome * imports
- Biostrings * imports
- GenomicRanges * imports
- IRanges * imports
- Rcpp * imports
- S4Vectors * imports
- data.table * imports
- formattable * imports
- future.apply * imports
- methods * imports
- pwalign * imports
- stats * imports
- stringi * imports
- stringr * imports
- utils * imports
- BSgenome.Hsapiens.UCSC.hg38 * suggests
- BiocStyle * suggests
- knitr * suggests
- markdown * suggests
- pander * suggests
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- testthat * suggests