Selfish

Selfish is a software tool for the comparative analysis of Hi-C data, which are genome-wide maps of chromatin interactions obtained from high-throughput conformation capture experiments. The main goal of Selfish is to help life scientists investigate the role of the three-dimensional structure of genomes in gene regulation and other essential cellular functions by comparing two contact maps derived from Hi-C experiments.

The key features of Selfish are:

1. It introduces a novel self-similarity measure that takes advantage of the structural self-similarity in contact maps, enabling more accurate and robust comparisons.

2. It provides algorithms for measuring the reproducibility of Hi-C replicate experiments, allowing researchers to evaluate the consistency and reliability of their data.

3. It enables the identification of differential chromatin interactions between two contact maps, helping researchers pinpoint genomic regions with potential biological significance.

Selfish addresses the challenges in the comparative analysis of Hi-C data, which arise from the complexity of chromatin conformations and technology-driven and sequence-specific biases.