Metacoder: An R package for visualization and manipulation of community taxonomic diversity data. - Zachary S. L. Foster; Thomas J. Sharpton; Niklaus J. Grünwald (PLoS Comput. Biol., 2017)

Taxa: An R package implementing data standards and methods for taxonomic data. - Zachary S. L. Foster; Scott Chamberlain; Niklaus J. Grünwald (F1000Research, 2018)

Krisp: A Python package to aid in the design of CRISPR and amplification-based diagnostic assays from whole genome sequencing data. - Zachary S. L. Foster; Andrew S. Tupper; Caroline M. Press; Niklaus J. Grünwald (PLoS Comput. Biol., 2024)