|edgeR: a Bioconductor package for differential expression analysis of digital gene expression data|
MD Robinson, DJ McCarthy, GK Smyth
Bioinformatics 26 (1), 139-140, 2010
|Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation|
DJ McCarthy, Y Chen, GK Smyth
Nucleic acids research 40 (10), 4288-4297, 2012
|Count-based differential expression analysis of RNA sequencing data using R and Bioconductor|
S Anders, DJ McCarthy, Y Chen, M Okoniewski, GK Smyth, W Huber, ...
Nature protocols 8 (9), 1765, 2013
|The genetic architecture of type 2 diabetes|
C Fuchsberger, J Flannick, TM Teslovich, A Mahajan, V Agarwala, ...
Nature 536 (7614), 41-47, 2016
|Testing significance relative to a fold-change threshold is a TREAT|
DJ McCarthy, GK Smyth
Bioinformatics 25 (6), 765-771, 2009
|Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R|
DJ McCarthy, KR Campbell, ATL Lun, QF Wills
Bioinformatics 33 (8), 1179-1186, 2017
|A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor|
ATL Lun, DJ McCarthy, JC Marioni
F1000Research 5, 2016
|Factors influencing success of clinical genome sequencing across a broad spectrum of disorders|
JC Taylor, HC Martin, S Lise, J Broxholme, JB Cazier, A Rimmer, ...
Nature genetics 47 (7), 717-726, 2015
|Common genetic variation drives molecular heterogeneity in human iPSCs|
H Kilpinen, A Goncalves, A Leha, V Afzal, K Alasoo, S Ashford, S Bala, ...
Nature 546 (7658), 370-375, 2017
|Classification of low quality cells from single-cell RNA-seq data|
T Ilicic, JK Kim, AA Kolodziejczyk, FO Bagger, DJ McCarthy, JC Marioni, ...
Genome biology 17 (1), 29, 2016
|Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates|
SP Lund, D Nettleton, DJ McCarthy, GK Smyth
Statistical applications in genetics and molecular biology 11 (5), 2012
|Choice of transcripts and software has a large effect on variant annotation|
DJ McCarthy, P Humburg, A Kanapin, MA Rivas, K Gaulton, JB Cazier, ...
Genome medicine 6 (3), 26, 2014
|Whole-genome sequencing of bladder cancers reveals somatic CDKN1A mutations and clinicopathological associations with mutation burden|
JB Cazier, SR Rao, CM McLean, AK Walker, BJ Wright, EEM Jaeger, ...
Nature communications 5 (1), 1-13, 2014
|f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq|
F Buettner, N Pratanwanich, DJ McCarthy, JC Marioni, O Stegle
Genome biology 18 (1), 212, 2017
|NOX1 loss-of-function genetic variants in patients with inflammatory bowel disease|
T Schwerd, RV Bryant, S Pandey, M Capitani, L Meran, JB Cazier, J Jung, ...
Mucosal immunology 11 (2), 562-574, 2018
|Aliskiren increases bradykinin and tissue kallikrein mRNA levels in the heart|
DJ Campbell, Y Zhang, DJ Kelly, RE Gilbert, DJ McCarthy, W Shi, ...
Clinical and Experimental Pharmacology and Physiology 38 (9), 623-631, 2011
|Differential Expression for RNA Sequencing (RNA-Seq) Data: Mapping, Summarization, Statistical Analysis, and Experimental Design|
MD Young, DJ McCarthy, MJ Wakefield, GK Smyth, A Oshlack, ...
Bioinformatics for High Throughput Sequencing, 169-190, 2012
|MOZ and BMI1 play opposing roles during Hox gene activation in ES cells and in body segment identity specification in vivo|
BN Sheikh, NL Downer, B Phipson, HK Vanyai, AJ Kueh, DJ McCarthy, ...
Proceedings of the National Academy of Sciences 112 (17), 5437-5442, 2015
|Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity|
SM Linker, L Urban, SJ Clark, M Chhatriwala, S Amatya, DJ McCarthy, ...
Genome biology 20 (1), 30, 2019
|Visualization of biomedical data|
SI O'Donoghue, BF Baldi, SJ Clark, AE Darling, JM Hogan, S Kaur, ...
Annual Review of Biomedical Data Science 1, 275-304, 2018