Davis J McCarthy
Davis J McCarthy
Head, Bioinformatics and Cellular Genomics, St Vincent's Institute of Medical Research
Verified email at svi.edu.au - Homepage
Title
Cited by
Cited by
Year
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
224472010
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
31592012
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
10552013
The genetic architecture of type 2 diabetes
C Fuchsberger, J Flannick, TM Teslovich, A Mahajan, V Agarwala, ...
Nature 536 (7614), 41-47, 2016
9102016
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
7102017
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
6852016
Testing significance relative to a fold-change threshold is a TREAT
DJ McCarthy, GK Smyth
Bioinformatics 25 (6), 765-771, 2009
4792009
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), 1-15, 2016
3572016
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
3542017
Eleven grand challenges in single-cell data science
D Lähnemann, J Köster, E Szczurek, DJ McCarthy, SC Hicks, ...
Genome biology 21 (1), 1-35, 2020
2912020
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
2912015
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
2522012
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), 1-16, 2014
1742014
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
1302014
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
1182020
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), 1-13, 2017
782017
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), 1-14, 2020
772020
Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference
Y Huang, DJ McCarthy, O Stegle
Genome biology 20 (1), 1-12, 2019
452019
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
432018
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
422018
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Articles 1–20