From reads to regions: a Bioconductor workflow to detect differential binding in ChIP-seq data [version 2; referees: 2 approved, 1 approved with reservations]

by Aaron T. L. Lun, Gordon K. Smyth
Published 2016-01-01

From reads to regions: a Bioconductor workflow to detect differential binding in ChIP-seq data [version 1; referees: 2 approved, 1 approved with reservations]

by Aaron T. L. Lun, Gordon K. Smyth
Published 2015-10-01

beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types.

by Aaron T L Lun, Hervé Pagès, Mike L Smith
Published 2018-05-01

Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments [version 1; referees: 2 approved]

by Aaron T. L. Lun, Malcolm Perry, Elizabeth Ing-Simmons
Published 2016-05-01

Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments [version 2; referees: 2 approved]

by Aaron T. L. Lun, Malcolm Perry, Elizabeth Ing-Simmons
Published 2016-06-01

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline [version 1; referees: 2 approved]

by Yunshun Chen, Aaron T. L. Lun, Gordon K. Smyth
Published 2016-06-01

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline [version 2; referees: 5 approved]

by Yunshun Chen, Aaron T. L. Lun, Gordon K. Smyth
Published 2016-08-01

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor [version 2; referees: 1 approved, 4 approved with reservations]

by Aaron T.L. Lun, Davis J. McCarthy, John C. Marioni
Published 2016-10-01

iSEE: Interactive SummarizedExperiment Explorer [version 1; referees: 2 approved]

by Kevin Rue-Albrecht, Federico Marini, Charlotte Soneson, Aaron T.L. Lun
Published 2018-06-01

Detection and removal of barcode swapping in single-cell RNA-seq data

by Jonathan A. Griffiths, Arianne C. Richard, Karsten Bach, Aaron T. L. Lun, John C. Marioni
Published 2018-07-01

Transcriptome and H3K27 tri-methylation profiling of Ezh2-deficient lung epithelium

by Aliaksei Z. Holik, Laura A. Galvis, Aaron T.L. Lun, Matthew E. Ritchie, Marie-Liesse Asselin-Labat
Published 2015-09-01

EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data

by Aaron T. L. Lun, Samantha Riesenfeld, Tallulah Andrews, The Phuong Dao, Tomas Gomes, participants in the 1st Human Cell Atlas Jamboree, John C. Marioni
Published 2019-03-01

Genome-wide analysis reveals no evidence of trans chromosomal regulation of mammalian immune development.

by Timothy M Johanson, Hannah D Coughlan, Aaron T L Lun, Naiara G Bediaga, Gaetano Naselli, Alexandra L Garnham, Leonard C Harrison, Gordon K Smyth, Rhys S Allan
Published 2018-06-01

A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division

by Lovorka Stojic, Aaron T. L. Lun, Patrice Mascalchi, Christina Ernst, Aisling M. Redmond, Jasmin Mangei, Alexis R. Barr, Vicky Bousgouni, Chris Bakal, John C. Marioni, Duncan T. Odom, Fanni Gergely
Published 2020-04-01

RUNX2 Mediates Plasmacytoid Dendritic Cell Egress from the Bone Marrow and Controls Viral Immunity

by Michaël Chopin, Simon P. Preston, Aaron T.L. Lun, Julie Tellier, Gordon K. Smyth, Marc Pellegrini, Gabrielle T. Belz, Lynn M. Corcoran, Jane E. Visvader, Li Wu, Stephen L. Nutt
Published 2016-04-01

Isolation and Comparative Transcriptome Analysis of Human Fetal and iPSC-Derived Cone Photoreceptor Cells

by Emily Welby, Jorn Lakowski, Valentina Di Foggia, Dimitri Budinger, Anai Gonzalez-Cordero, Aaron T.L. Lun, Michael Epstein, Aara Patel, Elisa Cuevas, Kamil Kruczek, Arifa Naeem, Federico Minneci, Mike Hubank, David T. Jones, John C. Marioni, Robin R. Ali, Jane C. Sowden
Published 2017-12-01