nucleR

nucleR identifies nucleosome positions from next-generation sequencing (NGS) and tiling array data to characterize chromatin organization.

Key Features:

• Integration with R/Bioconductor: Interfaces with standard high-throughput genomics packages within the R/Bioconductor environment.
• Flexible and fast analysis: Implements algorithms for rapid and adaptable nucleosome positioning analysis of large NGS and tiling array datasets.
• In situ visualization: Visualizes nucleosome positions within the R environment.
• Export to genome browser formats: Exports analysis results to common genome browser formats.

Scientific Applications:

• Epigenomics: Characterizes nucleosome positioning to study chromatin structure and epigenetic regulation.
• Gene regulation: Infers nucleosome arrangements that influence gene expression.
• DNA replication and repair: Analyzes nucleosome positioning relevant to DNA replication and repair processes.
• NGS and tiling array data analysis: Applies to experimental workflows using next-generation sequencing and tiling arrays.

Methodology:

Computational algorithms identify nucleosome positions from sequencing reads or tiling array signals, and integration with R/Bioconductor enables application of statistical and graphical tools.