RiboProfiling

RiboProfiling analyzes ribosome profiling (Ribo-seq) data to process aligned ribosome footprints, quantify translation at the transcript level, identify amino-acid and multi-amino-acid motif-specific ribosome accumulations, and generate summary outputs for downstream statistical analysis.

Key Features:

• Input Handling: Accepts BAM files (binary Sequence Alignment/Map) containing aligned ribosome footprint data.
• Quality Assessment: Provides functions to assess the quality of Ribo-seq experiments.
• Footprint Quantification: Quantifies ribosome footprints at the transcript level to analyze translation dynamics across transcripts.
• Motif Identification: Identifies accumulation patterns of ribosome footprints on specific amino acids or multi-amino-acid motifs to detect translational regulation and ribosome pausing.
• Data Visualization and Reporting: Generates summary graphs and data quantifications representing analysis results.
• Statistical Analysis Integration: Integrates with Bioconductor packages to enable advanced modeling and statistical analysis of outputs.

Scientific Applications:

• Differential translation detection: Identifies differentially translated transcripts under varying experimental conditions.
• Ribosome pausing and codon-motif analysis: Detects ribosome pausing on specific codon motifs and pinpoints codon-motif accumulations.
• Comparative translation studies: Explores translation dynamics across organisms, exemplified by analyses with Escherichia coli data.

Methodology:

Implemented in R, RiboProfiling processes BAM-aligned Ribo-seq reads with initial quality assessment, transcript-level footprint quantification, motif identification, and outputs prepared for statistical evaluation via Bioconductor.