scanMiRApp

scanMiRApp provides a Shiny interface to the scanMiR package for scanning transcripts and custom sequences for miRNA binding sites, visualizing KdModels and binding results, and browsing predicted repression data.

Key Features:

• Transcript and sequence scanning: Scans transcripts and custom sequences for miRNA binding sites.
• KdModel visualization: Visualizes KdModels and binding results.
• Repression data browsing: Enables browsing of predicted repression data.
• IndexedFst class: Contains the IndexedFst class for fast indexed reading of large GenomicRanges or data.frames.
• Scan and enrichment utilities: Provides utilities for facilitating scans and identifying enriched miRNA-target pairs.

Scientific Applications:

• miRNA binding site prediction: Identifies miRNA binding sites in transcripts and custom sequences.
• miRNA-target interaction analysis: Supports identification of enriched miRNA-target pairs.
• Gene regulation studies: Facilitates investigation of predicted miRNA-mediated repression.

Methodology:

The application interfaces with the scanMiR package and implements fast indexed reading of large GenomicRanges or data.frames through the IndexedFst class.