GenomicPlot

GenomicPlot facilitates plotting of next generation sequencing data in bam, bed, wig, and bigwig formats, computing coverage and enrichment over input with respect to genomic features and user-defined loci for interpreting high-throughput genomics experiment results.

Key Features:

• Multi-format data import: Supports plotting of NGS data in bam, bed, wig, and bigwig formats.
• Coverage and enrichment computation: Computes and displays both coverage and enrichment over input with respect to genomic features including UTR, CDS, and enhancer, as well as user-defined genomic loci or regions.
• Statistical testing: Performs statistical tests on signal intensity within user-defined regions of interest, represented as boxplots or bar graphs.
• Parallel processing: Uses parallel processing to speed up computation on multicore platforms.
• Metagenomic plot generation: Generates metagenomic plots without introns for RNAseq or CLIPseq data in addition to genomic plots for ChIPseq data.

Scientific Applications:

• ChIPseq analysis: Displays coverage of genomic DNA for ChIPseq experiments.
• RNAseq analysis: Generates metagenomic plots without introns for RNAseq data visualization.
• CLIPseq analysis: Produces metagenomic plots without introns for CLIPseq data interpretation.
• High-throughput genomics interpretation: Enables visualization essential for interpreting high-throughput genomics experiment results.

Methodology:

Computes coverage and enrichment over input; performs statistical tests on signal intensity within user-defined regions of interest; uses parallel processing on multicore platforms.