pldist: ecological dissimilarities for paired and longitudinal microbiome association analysis. - Anna M. Plantinga; Jun Chen; Robert R. Jenq; Michael C. Wu (Bioinform., 2019)

aPCoA: covariate adjusted principal coordinates analysis. - Yushu Shi; Liangliang Zhang; Kim-Anh Do; Christine B. Peterson; Robert R. Jenq (Bioinform., 2020)

ProgPerm: Progressive permutation for a dynamic representation of the robustness of microbiome discoveries. - Liangliang Zhang; Yushu Shi; Kim-Anh Do; Christine B. Peterson; Robert R. Jenq (BMC Bioinform., 2021)

TARO: tree-aggregated factor regression for microbiome data integration. - Aditya K. Mishra; Iqbal Mahmud; Philip L. Lorenzi; Robert R. Jenq; Jennifer A Wargo; Nadim J. Ajami; Christine B. Peterson (Bioinform., 2024)

CAT: a conditional association test for microbiome data using a permutation approach. - Yushu Shi; Liangliang Zhang; Kim-Anh Do; Robert R. Jenq; Christine B. Peterson (Briefings Bioinform., 2025)