InPAS

InPAS identifies and refines alternative polyadenylation (APA) sites from RNAseq data to characterize 3' untranslated region (3' UTR) isoforms that influence mRNA stability, localization, and translation.

Key Features:

• Discovery of novel APA sites: InPAS processes RNAseq data to detect novel alternative polyadenylation (APA) sites and 3' UTR isoforms.
• Integration with cleanUpdTSeq: InPAS leverages cleanUpdTSeq to refine APA site calls and improve precision of site identification.
• Bioconductor and R environment: InPAS operates within the Bioconductor framework using R for statistical analysis of high-throughput genomic data.
• Interoperability: InPAS is compatible with other Bioconductor packages to enable integration into broader genomic analysis workflows.

Scientific Applications:

• Gene expression regulation studies: Identification of APA sites enables analysis of how alternative polyadenylation modulates gene expression via 3' UTR variation.
• Disease mechanism exploration: APA pattern analysis supports investigation of aberrant polyadenylation associated with conditions such as cancer and neurological disorders.
• Functional genomics research: Detection of 3' UTR isoforms facilitates studies of isoform-specific effects on mRNA stability, localization, and translation in cellular phenotypes.

Methodology:

Processes RNAseq data to detect APA events and applies cleanUpdTSeq to refine identified sites within the Bioconductor (R) environment.