netZooR

netZooR unifies the implementations of several Network Zoo methods into a single package by creating interfaces between network inference and network analysis methods.

Key Features:

• PANDA and OTTER: PANDA performs network reconstruction, and OTTER provides an optimized implementation using multiple lines of biological evidence.
• LIONESS: Performs single-sample network inference.
• EGRET: Infers genotype-specific networks.
• CONDOR: Performs community detection in networks.
• ALPACA: Performs differential community detection.
• CRANE: Estimates significance of differential modules.
• MONSTER: Estimates network transition states.
• YARN: Processes gene expression data for tissue-specific analyses.
• SAMBAR: Infers missing mutation data based on pathway information.

Scientific Applications:

• Network inference: Reconstructs gene regulatory networks from multiple data types including single-sample and genotype-specific contexts.
• Network analysis: Detects communities, differential communities, and significant differential modules, and estimates network transition states.
• Gene expression processing: Processes gene expression data for tissue-specific analyses.
• Mutation data inference: Infers missing mutation data using pathway information.

Methodology:

netZooR creates interfaces between network inference and network analysis methods. Network inference methods include PANDA, OTTER, LIONESS, and EGRET. Network analysis methods include CONDOR, ALPACA, CRANE, and MONSTER.