RiboR

RiboR provides programmatic access for analysis of ribosome profiling data, enabling length-resolved interrogation of ribosome-protected footprints stored in the 'ribo' binary file format.

Key Features:

• Ribo file format: Reads and writes the 'ribo' binary file format that stores ribosome-protected footprint data grouped by footprint length and associated metrics.
• Integration with RiboFlow pipeline: Integrates with RiboFlow pipeline outputs to analyze raw ribosome profiling sequencing data processed into 'ribo' files, with RiboFlow supporting parallelization.
• R and Python programmatic interfaces: Exposes programmatic interfaces in R (RiboR) and Python (RiboPy) to access quality control metrics, generate plots, and analyze ribosome occupancy across footprint lengths.

Scientific Applications:

• Protein abundance estimation: Uses ribosome occupancy measurements to estimate protein abundance levels.
• Translation mechanism inference: Enables inference of translation dynamics and regulation from length-resolved ribosome profiling data.

Methodology:

Operates by reading and writing 'ribo' files that encapsulate metrics for different ribosome footprint lengths.