Structstrings
:package: Structstrings: implementation of Biostrings to work with dot bracket annotations
Science Score: 49.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 10 DOI reference(s) in README -
○Academic publication links
-
✓Committers with academic emails
1 of 4 committers (25.0%) from academic institutions -
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (12.1%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
:package: Structstrings: implementation of Biostrings to work with dot bracket annotations
Basic Info
- Host: GitHub
- Owner: FelixErnst
- Language: R
- Default Branch: devel
- Homepage: https://felixernst.github.io/Structstrings/
- Size: 399 KB
Statistics
- Stars: 5
- Watchers: 1
- Forks: 0
- Open Issues: 1
- Releases: 0
Topics
Metadata Files
README.md
Structstrings: implementation of the dot bracket annotations with Biostrings 
<!-- badges: end -->
The Structstrings package implements the widely used dot bracket annotation for
storing base pairing information in structured RNA. For example it is heavily
used in the ViennaRNA (Lorenz et al. 2011) package, the tRNAscan-SE
(Lowe et al. 1997) software and the tRNAdb
(Juehling et al. 2009).
Structstrings uses the infrastructure provided by the
Biostrings package and derives the class DotBracketString and
related classes from the BString class. From these base pair tables can be
produced for in depth analysis, for which the DotBracketDataFrame class
is derived from the DataFrame class. In addition, the loop indices of the base
pairs can be retrieved as a LoopIndexList, a derivate of the IntegerList
class. Generally, all classes check automatically for the validity of the base
pairing information.
The conversion of the DotBracketString to the base pair table and the loop
indices is implemented in C for efficiency. The C implementation is inspired
by the ViennaRNA package to a large extent.
This package was developed as an improvement for the tRNA package. However,
other projects might benefit as well, so it was split of and improved upon.
Installation
The current version of the Structstrings package is available from
Bioconductor.
```{r}
Installation
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("Structstrings")
Load and attach the package
library("Structstrings") ```
Functions
Please have a look at vignette for details on the provided functions.
Literature
- Lorenz, Ronny; Bernhart, Stephan H.; Höner zu Siederdissen, Christian; Tafer, Hakim; Flamm, Christoph; Stadler, Peter F.; Hofacker, Ivo L. (2011): "ViennaRNA Package 2.0". Algorithms for Molecular Biology 6:26. doi:10.1186/1748-7188-6-26
- Lowe, T.M.; Eddy, S.R.(1997): "tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence". Nucl. Acids Res. 25: 955-964. doi:10.1093/nar/25.5.955
- Jühling, Frank; Mörl, Mario; Hartmann, Roland K.; Sprinzl, Mathias; Stadler, Peter F.; Pütz, Joern (2009): "TRNAdb 2009: Compilation of tRNA Sequences and tRNA Genes." Nucleic Acids Research 37 (suppl_1): D159–D162. doi:10.1093/nar/gkn772.
- Pagès, H.; Aboyoun, P.; Gentleman, R.; DebRoy, S. (2018). "Biostrings: Efficient manipulation of biological strings." R package version 2.50.1.
Owner
- Name: Felix Ernst
- Login: FelixErnst
- Kind: user
- Repositories: 35
- Profile: https://github.com/FelixErnst
GitHub Events
Total
- Watch event: 1
- Issue comment event: 2
- Push event: 2
- Create event: 1
Last Year
- Watch event: 1
- Issue comment event: 2
- Push event: 2
- Create event: 1
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| FelixErnst | f****t@o****m | 89 |
| Nitesh Turaga | n****a@g****m | 14 |
| J Wokaty | j****y@s****u | 10 |
| Hervé Pagès | h****s@f****g | 4 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 1
- Total pull requests: 2
- Average time to close issues: N/A
- Average time to close pull requests: less than a minute
- Total issue authors: 1
- Total pull request authors: 1
- Average comments per issue: 2.0
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- brendanf (1)
Pull Request Authors
- FelixErnst (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 14,793 total
- Total dependent packages: 3
- Total dependent repositories: 0
- Total versions: 6
- Total maintainers: 1
bioconductor.org: Structstrings
Implementation of the dot bracket annotations with Biostrings
- Homepage: https://github.com/FelixErnst/Structstrings
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/Structstrings/inst/doc/Structstrings.pdf
- License: Artistic-2.0
-
Latest release: 1.24.0
published 10 months ago