VplotR

VplotR generates V-plots and computes footprint profiles to analyze patterns of paired-end sequencing fragment density for inferring protein locations from DNA nuclease digestion and protection patterns.

Key Features:

• V-plot generation: Creates V-plots over single or aggregated genomic loci of interest.
• Footprint profile computation: Computes footprint profiles over single or aggregated genomic loci of interest.
• Paired-end sequencing fragment density analysis: Analyzes patterns of paired-end sequencing fragment density.

Scientific Applications:

• Protein localization inference: Infers the location of associated proteins from patterns of digestion and protection from DNA nucleases including DNAse I, micrococcal nuclease, and Tn5 transposase.
• Genomic locus analysis: Examines protein-DNA interactions at single or aggregated genomic regions of interest.

Methodology:

VplotR analyzes patterns of paired-end sequencing fragment density to generate V-plots and footprint profiles over genomic loci.