methylKit

"methylKit" is an R package developed to facilitate the analysis of genome-wide cytosine epigenetic profiles derived from high-throughput methylation and hydroxymethylation sequencing experiments. DNA methylation, a critical chemical modification of cytosine bases, plays a significant role in gene regulation, cellular differentiation, and cancer pathogenesis. Given the complexity and volume of data generated in methylation studies, methylKit provides a comprehensive suite of tools to streamline the analysis process.

The package offers functionalities for clustering, sample quality visualization, differential methylation analysis, and annotation features. Collectively, these tools automate many steps in identifying statistically significant bases or regions of DNA methylation, thereby simplifying the process of drawing meaningful biological conclusions from the data.