RNAvigate

RNAvigate enables efficient exploration of RNA chemical probing datasets through automated parsing of multiple file formats and generation of diverse plot types for analyzing RNA structure information and experimental conditions.

Key Features:

• File Format Parsing: Automatically parses 21 standard file formats including primary sequence annotations, per- and internucleotide data, and secondary and tertiary structures.
• Plot Generation: Outputs 18 plot types for visualizing RNA structural data and relationships.
• Multi-condition Analysis: Enables exploration of nuanced relationships between multiple layers of RNA structure information and across multiple experimental conditions.
• Jupyter Notebook Compatibility: Supports reproducible, transparent, and organized sharing of multistep analyses and data visualization strategies.

Scientific Applications:

• RNA Structure Analysis: Examines local nucleotide flexibility, RNA secondary structure, and multistate structural ensembles from chemical probing data.
• Interaction Mapping: Analyzes protein and ligand binding and through-space interaction networks.
• Structure-Function Relationship Studies: Evaluates RNA systems under structure- and function-altering conditions with linked multilayered data visualization.
• Integrative Data Exploration: Facilitates iteration on integrative analyses of diverse, complex RNA chemical probing datasets.

Methodology:

RNAvigate is implemented as a Python library that parses input file formats and generates plot types for RNA chemical probing data analysis.