Smoother

Smoother facilitates dynamic, on-the-fly analysis and visualization of nucleic acid interactome datasets, including chromosome conformation capture (Hi-C) and RNA–DNA interaction data, to support exploratory parameter tuning and comparative interactome analysis.

Key Features:

• Dynamic Parameter Adjustment: Allows interactive modification of analysis parameters such as normalization techniques (e.g., iterative correction), bin size, and mapping quality (MAPQ) without rerunning pipelines.
• Sparse Prefix Sum Index: Employs a sparse prefix sum index to enable rapid, on-the-fly processing of large interactome datasets.
• Interactive Filtering and Comparison: Supports filtering by mapping quality and near-instantaneous comparisons between different normalization approaches and ploidy corrections.
• Overlay and Annotation Capabilities: Enables overlay of additional sequencing data and genomic annotations and filtering by those annotations on interactome views.
• Multi-Sample Comparison: Supports loading, grouping, and comparative analysis of multiple samples or replicates.
• Virtual 4C Analysis: Facilitates virtual 4C assays to examine interactions around specific genomic loci using existing interactome data.

Scientific Applications:

• Chromatin architecture studies: Enables interactive exploration of Hi-C contact patterns to investigate three-dimensional genome organization.
• Gene regulation research: Supports analysis of RNA–DNA interactions and contact profiles to study regulatory interactions affecting gene expression.
• Comparative genome organization: Facilitates multi-sample comparisons and ploidy-corrected analyses to study differences in genome organization across conditions or samples.

Methodology:

Smoother leverages a sparse prefix sum index for fast, on-the-fly data processing and real-time visualization while supporting interactive adjustment of parameters including normalization (e.g., iterative correction), bin size, MAPQ filtering, ploidy corrections, and virtual 4C computations.