clipplotr-a comparative visualization and analysis tool for CLIP data

Area of Science:

• Molecular Biology
• Bioinformatics
• Genomics

Background:

• Cross-linked immunoprecipitation (CLIP) technologies are crucial for studying RNA-protein interactions, generating extensive public datasets.
• Analyzing CLIP data requires visual inspection and comparison across conditions or datasets, often necessitating further data processing.
• Integrating CLIP signals with genomic annotations and functional data (e.g., RNA-seq) is essential for deriving biological insights.

Purpose of the Study:

• To develop a user-friendly command-line tool, clipplotr, for enhanced visualization and comparative analysis of CLIP data.
• To enable seamless integration of CLIP data with reference annotations and orthogonal functional genomic data.
• To provide normalization and smoothing options for CLIP data to facilitate robust analysis.

Main Methods:

• Developed clipplotr, a command-line tool written in R.
• Implemented options for data normalization and smoothing.
• Designed the tool to accept various input file formats for CLIP data, annotations, and functional genomics data.

Main Results:

• clipplotr facilitates visual comparative and integrative analyses of CLIP data.
• The tool generates publication-quality figures by combining CLIP signals with annotation and functional genomic tracks.
• clipplotr is versatile, runnable on laptops and high-performance clusters, and supports diverse data inputs.

Conclusions:

• clipplotr simplifies the exploration and interpretation of CLIP-seq datasets.
• The tool enhances the ability to perform comparative and integrative analyses, aiding biological discovery.
• clipplotr is freely available with source code and documentation, promoting accessibility and reproducibility.