clipplotr

clipplotr visualizes and compares Cross-Linking Immunoprecipitation (CLIP) datasets to inspect RNA–protein interactions across genes or genomic regions.

Key Features:

• Comparative Visualization: Plots multiple CLIP tracks over a gene or genomic region to enable direct comparisons within projects or with public datasets.
• Normalization and Smoothing: Applies various normalization and smoothing techniques to processed CLIP signal traces.
• Integration with Additional Data Types: Displays reference annotation tracks and other functional genomic datasets such as RNA-seq alongside CLIP data.
• Flexible Input Formats: Accepts a range of input file formats for CLIP and related genomic data.
• High-Quality Output: Exports publication-quality figures of CLIP and integrated tracks.
• Implementation: Implemented in R as a command-line application for incorporation into computational workflows.

Scientific Applications:

• Gene Regulation Analysis: Compare CLIP and RNA-seq data to investigate RNA–protein interactions that influence gene regulation.
• RNA-Binding Site Identification: Visualize CLIP signal peaks to identify and validate RNA-binding sites.
• Condition-Specific Interaction Analysis: Detect condition- or dataset-specific changes in RNA–protein interactions through track comparisons.
• Integrative Functional Interpretation: Combine CLIP with annotations and RNA-seq to derive functional insights from CLIP experiments.

Methodology:

Implemented in R as a command-line application that accepts multiple input file formats, applies normalization and smoothing to processed CLIP data, plots multiple CLIP tracks alongside reference annotations and RNA-seq, and exports publication-quality figures; it can be integrated into larger computational workflows including high-performance clusters.