ggcoverage

ggcoverage visualizes and annotates genome coverage from next-generation sequencing (NGS) data to support interpretation of WGS, WES, RNA-seq, ChIP-seq, and protein coverage experiments.

Key Features:

• Multi-Format Input Support: Accepts BAM, BigWig, BedGraph, and TSV files for coverage and track data.
• Comprehensive Annotation Capabilities: Provides annotation overlays tailored to WGS, WES, RNA-seq, ChIP-seq, and protein coverage and supports combining annotations using the '+' operator.
• Advanced Preprocessing Tools: Implements read normalization, consensus peak generation, and track data loading.
• Customizable Visualization: Constructs publication-quality, highly customizable plots using ggplot2.
• Multi-Omics and Multi-Group Support: Handles datasets comprising multiple groups and omics layers for integrated comparisons.

Scientific Applications:

• Genomics: Visualization and annotation of genome coverage in whole-genome and whole-exome sequencing studies.
• Transcriptomics: Visualization and annotation of RNA-seq coverage.
• Epigenetics: Visualization and annotation of ChIP-seq and other epigenetic coverage data.
• Proteomics: Visualization and annotation of protein coverage data.
• Multi-omics integration: Integrated visualization and comparison across multiple omics layers and groups.

Methodology:

Reads BAM, BigWig, BedGraph, and TSV inputs; performs read normalization, consensus peak generation, and track data loading; overlays annotations via the '+' operator; and renders plots with ggplot2.