Davis J McCarthy
Davis J McCarthy
Head, Bioinformatics and Cellular Genomics, St Vincent's Institute of Medical Research
Verified email at - Homepage
Cited by
Cited by
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
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
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
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
The genetic architecture of type 2 diabetes
C Fuchsberger, J Flannick, TM Teslovich, A Mahajan, V Agarwala, ...
Nature 536 (7614), 41-47, 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
Testing significance relative to a fold-change threshold is a TREAT
DJ McCarthy, GK Smyth
Bioinformatics 25 (6), 765-771, 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
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
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
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
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
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
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
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
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
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
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
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
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