chimera

chimera consolidates outputs from fusion-detection algorithms (chimeraScan, bellerophontes, deFuse, FusionFinder, FusionHunter, FusionMap, mapSplice, Rsubread, tophat-fusion, and STAR) to organize, annotate, analyze, and validate gene fusion events for downstream characterization.

Key Features:

• Multi-tool input support: Accepts and consolidates outputs from chimeraScan, bellerophontes, deFuse, FusionFinder, FusionHunter, FusionMap, mapSplice, Rsubread, tophat-fusion, and STAR.
• Central fusion data structure: Stores fusion events detected by supported tools in a unified internal representation.
• Unified data format: Consolidates diverse detection outputs into a single format for downstream analysis.
• R integration: Implemented in R and enables manipulation of fusion data using standard R functions.
• Annotation and analysis functions: Provides specialized Chimera functions for annotation, analysis, and validation of fusion events.
• False-positive discrimination: Includes functionalities aimed at distinguishing true fusion events from false positives.

Scientific Applications:

• Fusion product characterization: Comprehensive characterization of fusion products to assess biological significance.
• Cancer genomics: Analysis and validation of gene fusions relevant to oncogenesis studies.
• Molecular biology and genetic disorders: Investigation of fusion events in broader molecular biology and genetic disorder contexts.
• Fusion-call validation: Generation of reliable insights through detailed analysis and validation of fusion data.

Methodology:

Implemented in R using a central fusion data structure that stores and consolidates outputs from the listed fusion-detection tools, with manipulation via standard R functions and specialized Chimera functions for annotation, analysis, validation, and discrimination of true versus false fusion events.