The sva package for removing batch effects and other unwanted variation in high-throughput experiments. - Jeffrey T. Leek; W. Evan Johnson; Hilary S. Parker; Andrew E. Jaffe; John D. Storey (Bioinform., 2012)

Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction. - Hilary S. Parker; Jeffrey T. Leek; Alexander V. Favorov; Michael Considine; Xiaoxin Xia; Sameer Chavan; Christine H. Chung; Elana J. Fertig (Bioinform., 2014)

AGA: Interactive pipeline for reproducible genomics analyses. - Michael Considine; Hilary S. Parker; Yingying Wei; Xaio Xia; Leslie Cope; Michael F. Ochs; Elana J. Fertig (F1000Research, 2015)