regioneR

regioneR performs statistical assessment of associations between sets of genomic regions and other genomic features using permutation tests and randomization-based approaches to accommodate the complexity of genomic and epigenomic data.

Key Features:

• Permutation Test Framework: Employs permutation tests tailored for genomic regions to assess associations between region sets and diverse genomic features.
• Custom randomization strategies and metrics: Supports user-defined randomization strategies and evaluation metrics to tailor statistical assessments to specific datasets.
• Local specificity evaluation: Provides a function to evaluate the local specificity of detected associations, identifying regions where associations are most pronounced.
• R package implementation: Implemented as an R package for integration with R-based genomic analysis workflows.

Scientific Applications:

• Genomic and epigenomic association testing: Assess spatial relationships between genomic region sets and annotations in genomic and epigenomic studies.
• Gene regulation studies: Evaluate overlaps and proximities relevant to regulatory elements and gene regulation mechanisms.
• Chromatin organization analysis: Test associations related to chromatin organization and spatial genome features.
• Spatial relationship analysis: Quantify and statistically validate spatial dependencies between region sets and other genomic features.

Methodology:

Uses permutation tests and randomization-based approaches, supports user-defined randomization strategies and evaluation metrics, and includes a function to evaluate local specificity of associations.