shannon: Information-Theoretic Analysis of Genomic Data

The shannon package provides tools for computing Jensen-Shannon divergence and other information-theoretic quantities for genomic position files (GPFs). It is particularly useful for analyzing DNA methylation diversity and other genomic features using Shannon entropy and related measures.

Main functions

• divergence: Computes within-group divergence for population

• js_divergence: Calculates Jensen-Shannon divergence

• shannon_entropy: Computes Shannon entropy

• get_regions: Gets regions for analysis

• get_data: Retrieves and combines genomic data

Data input

The package works with:

• Tabix-indexed genome position files (GPFs)

• Metadata tables specifying sample information

• BED-like format files

Author

Maintainer: Eylül Harputluoglu eyluelgoekce.harputluoglu@botinst.uzh.ch