carnation

carnation enables interactive exploration and management of RNA-Seq analyses through modular visualization of differential expression, functional enrichment, and gene pattern analysis.

Key Features:

• Differential Expression Visualization: Generates PCA plots, MA plots, Upset plots, heatmaps, and customizable gene plots for DE analysis.
• Functional Enrichment Visualization: Provides seven distinct visualization types for functional enrichment analysis.
• Gene Pattern Analysis: Supports pattern analysis of gene expression across conditions or samples.
• Gene Scratchpad: Allows tracking of genes of interest across all analytical modules.

Scientific Applications:

• RNA-Seq Differential Expression Analysis: Visualizes and explores differentially expressed genes from RNA-Seq experiments through multiple plot types.
• Functional Enrichment Exploration: Interprets biological meaning of gene sets through seven visualization methods for enrichment results.
• Gene Expression Pattern Discovery: Identifies and examines gene expression patterns across experimental conditions or samples.

Methodology:

The tool is implemented as a modular Shiny application with integrated project management and multi-user access capabilities for server-based collaborative deployment.