# DuplexDiscovereR <!-- badges: start --> <!-- badges: end --> 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](https://www.gnu.org/licenses/gpl-3.0.html). The documentation, including the manual pages and vignettes, is distributed under a [CC BY-SA 4.0 license](https://creativecommons.org/licenses/by-sa/4.0/deed.en). Some functionality of `DuplexDiscovereR` depends on the [RNAduplex](https://www.tbi.univie.ac.at/RNA/RNAduplex.1.html) from the [ViennaRNA](https://www.tbi.univie.ac.at/RNA/). 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](https://www.tbi.univie.ac.at/RNA/RNAduplex.1.html) can be installed by foolowing instructions on [ViennaRNA web-page](https://www.tbi.univie.ac.at/RNA/) ## Getting started See the tutorial by loading package vignette ```r browseVigenttes("DuplexDiscovereR") ``` ## Citataion *Not avaliable before paper publication*