A collection of bioinformatics tools used to analyze data generated using the CRSSANT/rna2d3d pipeline.
Advancements in the field of RNA structure and interaction studies have enabled high throughput analysis of RNAs, revealing base pairing and higher order interactions. Despite the progress on the experimental methods for studying RNA secondary and intermolecular complexes, computational analysis of such data generated has remained a challenge. One subset of such experimental methods, the crosslinking- and proximity-ligation based approaches generates non-continuous reads that indicate specific RNA structures and interactions. Here, we provide tools that help to make sense of the results generated from the computational pipeline used across myriad methods employing the crosslinking-ligation principle (see PARIS, PARIS2, SHARC).
Tools are available on the root directory of this repository. The description of each can be found built into their repsective help text (i.e., python3 script.py --help). For RNA2D3D specific tools, see thee rna2d3d_tools repository.
Project Link: https://whl-usc.github.io/