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 | 38297 | 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 | 5208 | 2012 |
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 | 1561 | 2016 |
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 | 1540 | 2017 |
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), 1765-1786, 2013 | 1321 | 2013 |
The genetic architecture of type 2 diabetes C Fuchsberger, J Flannick, TM Teslovich, A Mahajan, V Agarwala, ... Nature 536 (7614), 41-47, 2016 | 1275 | 2016 |
Eleven grand challenges in single-cell data science D Lähnemann, J Köster, E Szczurek, DJ McCarthy, SC Hicks, ... Genome biology 21, 1-35, 2020 | 1064 | 2020 |
Testing significance relative to a fold-change threshold is a TREAT DJ McCarthy, GK Smyth Bioinformatics 25 (6), 765-771, 2009 | 713 | 2009 |
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, 1-15, 2016 | 703 | 2016 |
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 | 619 | 2017 |
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 | 433 | 2015 |
Benchmarking single-cell RNA-sequencing protocols for cell atlas projects E Mereu, A Lafzi, C Moutinho, C Ziegenhain, DJ McCarthy, ... Nature biotechnology 38 (6), 747-755, 2020 | 387 | 2020 |
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 | 354 | 2012 |
Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data TS Andrews, VY Kiselev, D McCarthy, M Hemberg Nature protocols 16 (1), 1-9, 2021 | 269 | 2021 |
Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression ASE Cuomo, DD Seaton, DJ McCarthy, I Martinez, MJ Bonder, ... Nature communications 11 (1), 810, 2020 | 261 | 2020 |
Choice of transcripts and software has a large effect on variant annotation DJ McCarthy, P Humburg, A Kanapin, MA Rivas, K Gaulton, ... Genome medicine 6, 1-16, 2014 | 235 | 2014 |
Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference Y Huang, DJ McCarthy, O Stegle Genome biology 20, 1-12, 2019 | 202 | 2019 |
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), 3756, 2014 | 173 | 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, 1-13, 2017 | 136 | 2017 |
Visualization of biomedical data SI O'Donoghue, BF Baldi, SJ Clark, AE Darling, JM Hogan, S Kaur, ... Annual Review of Biomedical Data Science 1 (1), 275-304, 2018 | 100 | 2018 |