dirCLIP is a computational toolkit designed for analyzing and profiling RNA-protein interactions using nanopore sequencing data. This repository contains scripts and workflows used in the manuscript submitted to Nature Methods.
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Alignment/- Contains scripts and tools for aligning nanopore reads to reference genomes.
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Motif_analysis/- Includes R scripts for analyzing sequence motifs and CNNC distances from mutation sites.
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Mutation_profiling/- Provides Python and R scripts for identifying, grouping, and visualizing mutation sites across samples.
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Clone the repository:
git clone https://github.com/rnaomics/dirCLIP.git cd dirCLIP -
Navigate to the desired folder and run the scripts using Python or R:
To find dirCLIP sites using Mutation profiling, go to the folder Mutation profiling.
cd Mutation_profiling- Ensure required dependencies are installed (e.g., Bioconductor packages for R, pandas/numpy for Python).
This project is released under the MIT License.
For questions, please contact Mohamed Bahrudeen (mailto:mohamed.mohamedbahrdueen@tuni.fi).