FluShuffle and FluResort: new algorithms to identify reassorted strains of the influenza virus by mass spectrometry. - Aaron T. L. Lun; Jason W. H. Wong; Kevin M. Downard (BMC Bioinform., 2012)

diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data. - Aaron T. L. Lun; Gordon K. Smyth (BMC Bioinform., 2015)

Statistical analyses of high-throughput sequencing data to study chromatin structure and organisation. - Aaron T. L. Lun (2015)

It's DE-licious: A Recipe for Differential Expression Analyses of RNA-seq Experiments Using Quasi-Likelihood Methods in edgeR. - Aaron T. L. Lun; Yunshun Chen; Gordon K. Smyth (Statistical Genomics, 2016)

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline. - Yunshun Chen; Aaron T. L. Lun; Gordon K. Smyth (F1000Research, 2016)

Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments. - Aaron T. L. Lun; Malcolm Perry; Elizabeth Ing-Simmons (F1000Research, 2016)

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R. - Davis J. McCarthy; Kieran R. Campbell; Aaron T. L. Lun; Quin F. Wills (Bioinform., 2017)

iSEE: Interactive SummarizedExperiment Explorer. - Kevin C. Rue-Albrecht; Federico Marini 002; Charlotte Soneson; Aaron T. L. Lun (F1000Research, 2018)

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)

SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor. - Dario Righelli; Lukas M. Weber; Helena L. Crowell; Brenda Pardo; Leonardo Collado-Torres; Shila Ghazanfar; Aaron T. L. Lun; Stephanie C. Hicks; Davide Risso (Bioinform., 2022)

basilisk: a Bioconductor package for managing Python environments. - Aaron T. L. Lun (J. Open Source Softw., 2022)

Powering single-cell analyses in the browser with WebAssembly. - Aaron T. L. Lun; Jayaram Kancherla (J. Open Source Softw., 2023)

gesel: a JavaScript package for client-side gene set enrichment. - Aaron T. L. Lun; Jayaram Kancherla (J. Open Source Softw., 2023)