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)

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. - Lihua Julie Zhu; Claude Gazin; Nathan D. Lawson; Hervé Pagès; Simon M. Lin; David S. Lapointe; Michael R. Green (BMC Bioinform., 2010)

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)

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

beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types. - Aaron T. L. Lun; Hervé Pagès; Mike L. Smith (PLoS Comput. Biol., 2018)

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)

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)