RCAS

RCAS annotates genomic regions from RNA-based omics technologies to produce gene-centric annotations and analyses for functional interpretation of RNA-binding sites and transcriptomic targets.

Key Features:

• Implementation: Provided as an R package within the Bioconductor framework for integration with R/Bioconductor workflows.
• Input support: Processes genomic regions derived from CLIP-Seq, regions associated with RNA modifications (epitranscriptome), CAGE-tag locations, and other transcriptomic targets.
• Meta-gene profiles: Generates meta-gene profiles summarizing signal distribution across gene features.
• Gene-centric annotation: Produces detailed, gene-centered annotations linking regions to genomic features.
• Motif analysis: Performs sequence motif analysis to identify motifs associated with RNA-binding proteins or regulatory elements.
• Gene-set analysis: Conducts gene-set analyses to relate annotated regions to biological pathways and processes.
• Dynamic genome annotations and reporting: Produces dynamic genome annotations and reports for functional analysis of RNA-binding sites detected in high-throughput experiments.

Scientific Applications:

• Protein–RNA interaction analysis: Functional interpretation and annotation of binding sites derived from CLIP-Seq experiments.
• Epitranscriptome mapping: Annotation and analysis of genomic regions associated with RNA modifications.
• CAGE and transcriptomic target characterization: Characterization of CAGE-tag locations and other transcriptomic targets in a gene-centric context.
• Motif discovery for RBPs: Identification and analysis of sequence motifs linked to RNA-binding proteins.
• Pathway and gene-set interpretation: Linking annotated regions to gene sets and pathways to generate biological hypotheses and reproduce findings from published datasets.

Methodology:

Implemented as an R/Bioconductor package that processes input genomic regions to generate meta-gene profiles, gene-centric annotations, motif analyses, gene-set analyses, and dynamic genome annotation reports.