Searchlight2

Searchlight2 automates exploration, visualization, and interpretation of bulk RNA sequencing (RNA-seq) data following alignment, expression quantification, and differential expression analysis.

Key Features:

• Comprehensive statistical and visual analysis: Analyzes RNA-seq data at multiple biological levels, including global gene expression patterns, pathway-level analyses, and individual gene views.
• Workflow flexibility: Provides three distinct workflows that support various differential experimental designs across different organisms and experimental complexities.
• Automated reporting: Produces detailed, automated reports summarizing results and visualizations from analyses.
• R-script plot customization: Exports R scripts for downstream modification of plots and generation of manuscript-quality figures.
• Integration with standard pipelines: Operates downstream of alignment, expression quantification, and differential expression analysis and integrates with standard RNA-seq processing pipelines.
• Time efficiency: Can produce manuscript-quality figures in under three hours when used alongside standard RNA-seq processing pipelines.

Scientific Applications:

• Gene expression profiling: Summarizes and visualizes global and differential gene expression patterns from bulk RNA-seq experiments.
• Pathway analysis: Identifies and visualizes pathway-level changes linked to differential expression results.
• Single-gene investigation: Visualizes and interrogates expression patterns of individual genes.
• Complex experimental designs: Supports interpretation of studies with multiple conditions, contrasts, or organisms via specialized workflows.
• Figure generation and reporting: Produces manuscript-quality figures and comprehensive reports for downstream publication.

Methodology:

Operates on processed bulk RNA-seq data after alignment, expression quantification, and differential expression analysis, providing three workflows for distinct experimental designs, automated report generation, and exportable R scripts for plot modification.