This repository contains the raw data, processed data, and Jupyter notebooks used in the analysis of fpocketR and Frag-MaP data for the manuscript "Ligand-binding pocket in RNA, and where to find them".
Install instructions for the pocket detection, characterization, and visualization package used in the manuscript can be found at the fpocketR repository.
fpocketR use instructions can be found in the fpocketR repository demo
fpocketR results using default parameters.
fpocketR results using optimized parameters are available for the training set and test set.
Step-by-step printable protocol for Frag-MaP. Steps are included for cell culture through Illumina sequencing.
Raw sequencing data can be obtained at the GEO repository.
There are two options to view the analysis notebooks:
These are view-only versions of Jupyter Notebooks.
Frag-Mapper analysis used for:
Download this repository. In order to view the Jupyter notebooks, you will need Jupyter installed. In order to run them, you will need a Jupyter kernel with RNAvigate installed.
In future versions of RNAvigate, syntax changes may prevent these notebooks from running properly. If that is the case, here is the hard link to the version of RNAvigate used in these notebooks.