A package for the analysis of the data from RNA duplex probing experiments
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.
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.
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
library(devtools)
install_github('Egors01/DuplexDiscovereR')
RNAduplex can be installed by foolowing instructions on ViennaRNA web-page
Package tutorial is avaliable on Bioconductor
It can be loaded from R by
browseVigenttes("DuplexDiscovereR")
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}
}