GGtools: analysis of genetics of gene expression in bioconductor. - Vincent J. Carey; Martin Morgan; Seth Falcon; Ross Lazarus; Robert Gentleman (Bioinform., 2007)

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data. - Martin Morgan; Simon Anders; Michael F. Lawrence; Patrick Aboyoun; Hervé Pagès; Robert Gentleman (Bioinform., 2009)

Software for Computing and Annotating Genomic Ranges. - Michael F. Lawrence; Wolfgang Huber; Hervé Pagès; Patrick Aboyoun; Marc Carlson; Robert Gentleman; Martin T. Morgan; Vincent J. Carey (PLoS Comput. Biol., 2013)

VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants. - Valerie Obenchain; Michael F. Lawrence; Vincent J. Carey; Stephanie M. Gogarten; Paul Shannon; Martin Morgan (Bioinform., 2014)

Scalable Genomics with R and Bioconductor. - Michael F. Lawrence; Martin Morgan (CoRR, 2014)

Genomic Annotation Resources in R/Bioconductor. - Marc Carlson; Hervé Pagès; Sonali Arora; Valerie Obenchain; Martin Morgan (Statistical Genomics, 2016)

Public data and open source tools for multi-assay genomic investigation of disease. - Lavanya Kannan; Marcel Ramos; Angela Re; Nehme Hachem; Zhaleh Safikhani; Deena M. A. Gendoo; Sean Davis 001; David Gomez-Cabrero; Robert Castelo; Kasper D. Hansen; Vincent J. Carey; Martin Morgan; et al. (Briefings Bioinform., 2016)

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)

gwasurvivr: an R package for genome-wide survival analysis. - Abbas A. Rizvi; Ezgi Karaesmen; Martin Morgan; Leah Preus; Junke Wang; Michael Sovic; Theresa Hahn; Lara E. Sucheston-Campbell (Bioinform., 2019)

restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor. - Shweta Gopaulakrishnan; Samuela Pollack; BJ Stubbs; Hervé Pagès; John Readey; Sean Davis 001; Levi Waldron; Martin Morgan; Vincent J. Carey (F1000Research, 2019)

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)

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)

Toward a gold standard for benchmarking gene set enrichment analysis. - Ludwig Geistlinger; Gergely Csaba; Mara Santarelli; Marcel Ramos; Lucas Schiffer; Nitesh Turaga; Charity W. Law; Sean Davis 001; Vincent J. Carey; Martin Morgan; Ralf Zimmer; Levi Waldron (Briefings Bioinform., 2021)

Bioconductor toolchain for reproducible bioinformatics pipelines using Rcwl and RcwlPipelines. - Qiang Hu; Alan David Hutson; Song Liu; Martin Morgan; Qian Liu (Bioinform., 2021)

Evaluation of software impact designed for biomedical research: Are we measuring what's meaningful? - Awan Afiaz; Andrey Ivanov; John Chamberlin; David Hanauer; Candace Savonen; Mary J. Goldman; Martin Morgan; Michael Reich; Alexander Getka; Aaron Holmes; Sarthak Pati; Dan Knight; et al. (CoRR, 2023)

Curated single cell multimodal landmark datasets for R/Bioconductor. - Kelly B. Eckenrode; Dario Righelli; Marcel Ramos; Ricard Argelaguet; Christophe Vanderaa; Ludwig Geistlinger; Aedín C. Culhane; Laurent Gatto; Vincent J. Carey; Martin Morgan; Davide Risso; Levi Waldron (PLoS Comput. Biol., 2023)

ReUseData: an R/Bioconductor tool for reusable and reproducible genomic data management. - Qian Liu; Qiang Hu; Song Liu; Alan David Hutson; Martin Morgan (BMC Bioinform., 2024)