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

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

Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR [version 1; referees: 2 approved, 1 approved with reservations]

by Yunshun Chen, Bhupinder Pal, Jane E. Visvader, Gordon K. Smyth
Published 2017-11-01

Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR [version 2; referees: 2 approved, 1 approved with reservations]

by Yunshun Chen, Bhupinder Pal, Jane E. Visvader, Gordon K. Smyth
Published 2018-10-01

Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer

by Dharmesh D. Bhuva, Joseph Cursons, Gordon K. Smyth, Melissa J. Davis
Published 2019-11-01

Technical variability is greater than biological variability in a microarray experiment but both are outweighed by changes induced by stimulation.

by Penelope A Bryant, Gordon K Smyth, Roy Robins-Browne, Nigel Curtis
Published 2011-01-01

Detection of gene expression in an individual cell type within a cell mixture using microarray analysis.

by Penelope A Bryant, Gordon K Smyth, Roy Robins-Browne, Nigel Curtis
Published 2009-01-01

Correction: Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures

by Ran Blekhman, Alicia Oshlack, Adrien E. Chabot, Gordon K. Smyth, Yoav Gilad
Published 2009-03-01

Whole transcriptome analysis for T cell receptor-affinity and IRF4-regulated clonal expansion of T cells

by Wei Shi, Kevin Man, Gordon K. Smyth, Stephen L. Nutt, Axel Kallies
Published 2014-12-01

Gene regulation in primates evolves under tissue-specific selection pressures.

by Ran Blekhman, Alicia Oshlack, Adrien E Chabot, Gordon K Smyth, Yoav Gilad
Published 2008-11-01

Correction: Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures.

by Ran Blekhman, Alicia Oshlack, Adrien E. Chabot, Gordon K. Smyth, Yoav Gilad
Published 2009-03-01

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR [version 2; referees: 3 approved]

by Charity W. Law, Monther Alhamdoosh, Shian Su, Gordon K. Smyth, Matthew E. Ritchie
Published 2016-11-01

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR [version 1; referees: 3 approved]

by Charity W. Law, Monther Alhamdoosh, Shian Su, Gordon K. Smyth, Matthew E. Ritchie
Published 2016-06-01

qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data

by Necla Koçhan, G. Yazgi Tutuncu, Gordon K. Smyth, Luke C. Gandolfo, Göknur Giner
Published 2019-12-01

A guide to creating design matrices for gene expression experiments [version 1; peer review: 2 approved]

by Charity W. Law, Kathleen Zeglinski, Xueyi Dong, Monther Alhamdoosh, Gordon K. Smyth, Matthew E. Ritchie
Published 2020-12-01

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR [version 3; referees: 3 approved]

by Charity W. Law, Monther Alhamdoosh, Shian Su, Xueyi Dong, Luyi Tian, Gordon K. Smyth, Matthew E. Ritchie
Published 2018-12-01

Lung Basal Stem Cells Rapidly Repair DNA Damage Using the Error-Prone Nonhomologous End-Joining Pathway.

by Clare E Weeden, Yunshun Chen, Stephen B Ma, Yifang Hu, Georg Ramm, Kate D Sutherland, Gordon K Smyth, Marie-Liesse Asselin-Labat
Published 2017-01-01

Extracellular Vesicles in Synovial Fluid from Rheumatoid Arthritis Patients Contain miRNAs with Capacity to Modulate Inflammation

by Andrew D. Foers, Alexandra L. Garnham, Simon Chatfield, Gordon K. Smyth, Lesley Cheng, Andrew F. Hill, Ian P. Wicks, Ken C. Pang
Published 2021-05-01