DuplexDiscovereR
Science Score: 39.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 3 DOI reference(s) in README -
○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (11.7%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: Egors01
- Language: R
- Default Branch: master
- Size: 786 KB
Statistics
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 1
Metadata Files
README.md
DuplexDiscovereR
A package for the analysis of the data from RNA duplex probing experiments
About
DuplexDiscovereR is a package for analysing data from RNA cross-linking and proximity ligation protocols such as SPLASH, PARIS, LIGR-seq and other experimental methods that capture information about RNA-RNA interactions as chimeric fragments after high-throughput sequencing. It provides functions for uniform processing and visualisation of the raw chimeric read data. The methods implemented in DuplexDiscovereR are compatible with Bioconductor's GenomicRanges and InteractionSet classes, allowing for the integration of RNA-RNA interaction probing results into transcriptomic analyses.
License
The DuplexDiscovereR code is distributed under GNU Public License 3.0.
The documentation, including the manual pages and vignettes,
is distributed under a CC BY-SA 4.0 license.
Some functionality of DuplexDiscovereR depends on the RNAduplex from the
ViennaRNA. ViennaRNA is distributed under its own licence.
Installation
To install this package, use R (version "4.4"):
``` if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("DuplexDiscovereR") ```
You can also install the package from Github with
r
library(devtools)
install_github('Egors01/DuplexDiscovereR')
RNAduplex can be installed by foolowing instructions on ViennaRNA web-page
Getting started
Package tutorial is avaliable on Bioconductor
It can be loaded from R by
r
browseVigenttes("DuplexDiscovereR")
Citataion
Semenchenko E, Tsybulsky V, Meyer IM (2025). "DuplexDiscovereR: a computational method for the analysis of experimental duplex RNA-RNA interaction data". Nucleic Acids Research.
https://doi.org/10.1093/nar/gkaf266
@article{DuplexDiscovereR,
title={DuplexDiscovereR: a computational method for the analysis of experimental duplex RNA-RNA interaction data},
author={Semenchenko E, Tsybulsky V, Meyer IM},
journal={Nucleic Acids Research},
doi = {10.1093/nar/gkaf266}
year={2018},
publisher={Oxford University Press}
}
Owner
- Login: Egors01
- Kind: user
- Repositories: 1
- Profile: https://github.com/Egors01
GitHub Events
Total
- Create event: 5
- Issues event: 1
- Release event: 1
- Watch event: 2
- Delete event: 3
- Push event: 11
- Pull request event: 5
Last Year
- Create event: 5
- Issues event: 1
- Release event: 1
- Watch event: 2
- Delete event: 3
- Push event: 11
- Pull request event: 5
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 1
- Total pull requests: 13
- 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: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 13
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 4
- Average time to close issues: N/A
- Average time to close pull requests: 1 minute
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- Chao-Guo-hub (1)
Pull Request Authors
- Egors01 (18)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 1,906 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 2
- Total maintainers: 1
bioconductor.org: DuplexDiscovereR
Analysis of the data from RNA duplex probing experiments
- Homepage: https://github.com/Egors01/DuplexDiscovereR/
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/DuplexDiscovereR/inst/doc/DuplexDiscovereR.pdf
- License: GPL-3
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Latest release: 1.2.0
published about 1 year ago