iGenomicViewer: R package for visualisation of high dimension genomic data. - Daniel P. Gaile; Lori A. Shepherd; Andrew E. Bruno; Song Liu; Carl D. Morrison; Lara E. Sucheston; Jeffrey C. Miecznikowski (Int. J. Bioinform. Res. Appl., 2010)

Comparing Imputation Procedures for Affymetrix Gene Expression Datasets Using MAQC Datasets. - Sreevidya Sadananda Sadasiva Rao; Lori A. Shepherd; Andrew E. Bruno; Song Liu; Jeffrey C. Miecznikowski (Adv. Bioinformatics, 2013)

Orchestrating a community-developed computational workshop and accompanying training materials. - Sean Davis 001; Marcel Ramos; Lori A. Shepherd; Nitesh Turaga; Ludwig Geistlinger; Martin T. Morgan; Benjamin Haibe-Kains; Levi Waldron (F1000Research, 2018)

BiocPkgTools: Toolkit for mining the Bioconductor package ecosystem. - Shian Su; Vincent J. Carey; Lori A. Shepherd; Matthew E. Ritchie; Martin T. Morgan; Sean Davis 001 (F1000Research, 2019)

The Rockerverse: Packages and Applications for Containerization with R. - Daniel Nüst; Dirk Eddelbuettel; Dom Bennett; Robrecht Cannoodt; Dav Clark; Gergely Daroczi; Mark Edmondson; Colin Fay; Ellis Hughes; Sean Lopp; Ben Marwick; Heather Nolis; et al. (CoRR, 2020)

Tximeta: Reference sequence checksums for provenance identification in RNA-seq. - Michael I. Love; Charlotte Soneson; Peter F. Hickey; Lisa K. Johnson; N. Tessa Pierce; Lori A. Shepherd; Martin Morgan; Rob Patro (PLoS Comput. Biol., 2020)

The Rockerverse: Packages and Applications for Containerisation with R. - Daniel Nüst; Dirk Eddelbuettel; Dom Bennett; Robrecht Cannoodt; Dav Clark; Gergely Daroczi; Mark Edmondson; Colin Fay; Ellis Hughes; Lars Kjeldgaard; Sean Lopp; Ben Marwick; et al. (R J., 2020)

Eleven quick tips for writing a Bioconductor package. - Charlotte Soneson; Lori A. Shepherd; Marcel Ramos; Kevin C. Rue-Albrecht; Johannes Rainer; Hervé Pagès; Vincent J. Carey (PLoS Comput. Biol., 2025)