fedup

fedup tests for enrichment and depletion of user-defined pathways using Fisher's exact test, supporting custom pathway annotations in gmt, txt, and xlsx formats.

Key Features:

• Enrichment and Depletion Testing: Performs Fisher's exact test to detect both enriched and depleted pathways in user-defined gene sets.
• Versatile Input Format Support: Accepts pathway annotation files in gmt, txt, and xlsx formats for flexible custom annotation integration.
• Network Visualization: Integrates with Cytoscape to generate network-based pathway visualizations for enhanced result interpretability.

Scientific Applications:

• Custom Pathway Analysis: Enables pathway enrichment analysis on user-defined or non-standard pathway annotations beyond established databases.
• Functional Interpretation: Supports biological interpretation of gene lists through statistical testing of pathway membership.

Methodology:

Fisher's exact test is used to assess enrichment and depletion of user-defined pathways.