A computational tool to accurately identify footprints from bisulfite-sequencing data. MethylSeekR incorporates several methodological improvements and extensions that make it robust and generally applicable. The method is based on a cutoff approach that identifies hypomethylated regions as stretches of consecutive CpGs with methylation levels below a fixed threshold. To achieve high accuracy and sensitivity, MethylSeekR incorporates important preprocessing and filtering steps, and controls segmentation parameters via false discovery rate (FDR) calculations. MethylSeekR is an easy-to-use package that describes in detail each step of the analysis and produces several control plots to facilitate the interpretation of the results and to avoid potential pitfalls in the analysis.