soGGi

soGGi generates genomic interval aggregate and summary plots to visualize signal or motif occurrences from BAM and bigWig files and Bioconductor objects including Position Weight Matrices (PWM), run-length encoded lists (rlelist), GRanges, and GAlignments.

Key Features:

• Input support: Accepts BAM and bigWig files and Bioconductor objects such as Position Weight Matrices (PWM), run-length encoded lists (rlelist), GRanges, and GAlignments.
• Summary plot generation: Creates genomic interval aggregate and summary plots that represent signal or motif occurrences across regions.
• Normalization and transformation: Performs normalization, transformation, and arithmetic operations on summary plot objects.
• Grouping and subsetting: Supports grouping and subsetting of plots based on GRanges objects or user-supplied metadata.
• Plot rendering: Produces customizable plot outputs using ggplot2.
• Bioconductor integration: Operates within the Bioconductor ecosystem for interoperability with other R/Bioconductor packages.

Scientific Applications:

• Signal and motif visualization: Visualizes aggregate signal or motif distributions across genomic intervals.
• Comparative analysis: Enables comparison of datasets through normalization, transformation, and arithmetic operations on summary plots.
• Targeted regional analysis: Facilitates subgroup analyses by grouping or subsetting regions via GRanges or metadata.
• Publication-quality plotting: Generates plots suitable for reporting and figure preparation using ggplot2 customization.

Methodology:

Reads BAM and bigWig files and Bioconductor objects (PWM, rlelist, GRanges, GAlignments), computes genomic interval aggregate and summary plots, applies normalization, transformation, and arithmetic operations to summary plot objects, supports grouping/subsetting by GRanges or user-supplied metadata, and renders plots via ggplot2 within the Bioconductor ecosystem.