BEDOPS: high-performance genomic feature operations. - Shane J. Neph; Scott Kuehn; Alex P. Reynolds; Eric Haugen; Robert E. Thurman; Audra K. Johnson; Eric Rynes; Matthew T. Maurano; Jeff Vierstra; Sean Thomas; Richard S. Sandstrom; Richard Humbert; et al. (Bioinform., 2012)

eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data. - Charles E. Breeze; Alex P. Reynolds; Jenny van Dongen; Ian Dunham; John Lazar; Shane J. Neph; Jeff Vierstra; Guillaume Bourque; Andrew E. Teschendorff; John A. Stamatoyannopoulos; Stephan Beck 002 (Bioinform., 2019)