GenomicOZone

GenomicOZone clusters gene activity along chromosome into zones, detects differential zones as outstanding, and visualizes maps of outstanding zones across the genome to characterize effects on multiple genes within adaptive genomic neighborhoods.

Key Features:

• Chromosomal Zone Clustering: Clusters gene activity along chromosome into zones to identify regions of coordinated gene activity.
• Differential Zone Detection: Detects differential zones as outstanding to identify genomic regions with significantly altered gene activity.
• Genome-wide Visualization: Visualizes maps of outstanding zones across the genome to display spatial patterns of differential activity.
• Cluster Optimality Guarantee: Guarantees cluster optimality, linear runtime to sample size, and reproducibility in zone identification.
• Multi-omics Compatibility: Applies to genome-wide activity measurements including copy number, transcriptomic, proteomic, and methylation data.

Scientific Applications:

• Adaptive Genomic Neighborhood Characterization: Characterizes effects on multiple genes within adaptive genomic neighborhoods arising from genome reorganization, structural variation, or epigenome alteration.
• Copy Number Variation Analysis: Analyzes copy number data to identify zones of coordinated copy number alterations.
• Transcriptomic Zone Mapping: Maps transcriptomic data to detect chromosomal regions with coordinated differential gene expression.
• Proteomic Zone Detection: Detects zones of differential protein abundance across chromosomal regions.
• Methylation Zone Identification: Identifies zones of differential DNA methylation patterns along the genome.

Methodology:

The package clusters gene activity along chromosome into zones, detects differential zones as outstanding, and visualizes maps of outstanding zones across the genome with guaranteed cluster optimality and linear runtime to sample size.