ALTRE: workflow for defining ALTered Regulatory Elements using chromatin accessibility data. - Elizabeth Baskin; Rick Farouni; Ewy A. Mathé (Bioinform., 2017)

AmpUMI: design and analysis of unique molecular identifiers for deep amplicon sequencing. - Kendell Clement; Rick Farouni; Daniel E. Bauer; Luca Pinello (Bioinform., 2018)

Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements. - Luca Pinello; Rick Farouni; Guo-Cheng Yuan (Bioinform., 2018)