McCarthy, Davis J.

<tt>edgeR</tt> : a Bioconductor package for differential expression analysis of digital gene expression data

Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010) · Bioinformatics

Gene expression and cancer classificationGenomics and Phylogenetic Studies

Cited by 41,364

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

McCarthy, D. J., Chen, Y., & Smyth, G. K. (2012) · Nucleic Acids Research

Gene expression and cancer classificationGenomics and Phylogenetic Studies

Cited by 5,195

Scater: Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R

McCarthy, D. J., Campbell, K. R., Lun, A. T. L., & Wills, Q. F. (2017) · Bioinformatics

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 1,852

Eleven grand challenges in single-cell data science

Lähnemann, D., Köster, J., Szczurek, E., McCarthy, D. J., Hicks, S. C., Robinson, M. D., Vallejos, C. A., Campbell, K. R., Beerenwinkel, N., Mahfouz, A., et al. (2020) · Genome Biology

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 1,327

The genetic architecture of type 2 diabetes

Fuchsberger, C., Flannick, J., Teslovich, T. M., Mahajan, A., Agarwala, V., Gaulton, K. J., Ma, C., Fontanillas, P., Moutsianas, L., McCarthy, D. J., et al. (2016) · Nature

Genetic Associations and EpidemiologyGenetic Mapping and Diversity in Plants and Animals

Cited by 1,051

Classification of low quality cells from single-cell RNA-seq data

Ilicic, T., Kim, J. K., Kolodziejczyk, A. A., Bagger, F. O., McCarthy, D. J., Marioni, J. C., & Teichmann, S. A. (2016) · Genome Biology

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 693

Common genetic variation drives molecular heterogeneity in human iPSCs

Kilpinen, H., Goncalves, A., Leha, A., Afzal, V., Alasoo, K., Ashford, S., Bala, S., Bensaddek, D., Casale, F. P., Culley, O. J., et al. (2017) · Nature

Pluripotent Stem Cells ResearchGenetic Associations and Epidemiology

Cited by 586

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects

Mereu, E., Lafzi, A., Moutinho, C., Ziegenhain, C., McCarthy, D. J., Álvarez-Varela, A., Batlle, E., Sagar, Grün, D., Lau, J. K., et al. (2020) · Nature Biotechnology

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 499

Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference

Huang, Y., McCarthy, D. J., & Stegle, O. (2019) · Genome Biology

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 348

Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

Cuomo, A. S. E., Seaton, D. D., McCarthy, D. J., Martinez, I., Bonder, M. J., Garcia-Bernardo, J., Amatya, S., Madrigal, P., Isaacson, A., Buettner, F., et al. (2020) · Nature Communications

Pluripotent Stem Cells ResearchSingle-cell and spatial transcriptomics

Cited by 331

A comparison of marker gene selection methods for single-cell RNA sequencing data

Pullin, J. M., & McCarthy, D. J. (2022) · Genome biology

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 122

Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods

Neavin, D., Senabouth, A., Arora, H., Lee, J. T. H., Ripoll-Cladellas, A., sc-eQTLGen Consortium, Franke, L., Prabhakar, S., Ye, C. J., McCarthy, D. J., et al. (2024) · Genome Biology

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 90

Demuxafy : Improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods

Neavin, D., Senabouth, A., Hang Lee, J. T., Ripoll, A., sc-eQTLGen Consortium, Franke, L., Prabhakar, S., Ye, C. J., McCarthy, D. J., Melé, M., et al. (2022) · Genome biology

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 90

Case Report: Hypoglycemia Due to a Novel Activating Glucokinase Variant in an Adult – a Molecular Approach

Koneshamoorthy, A., Seniveratne-Epa, D., Calder, G., Sawyer, M., Kay, T. W. H., Farrell, S., Loudovaris, T., Mariana, L., McCarthy, D., Lyu, R., et al. (2022) · Frontiers in Endocrinology

Pancreatic function and diabetesDiabetes and associated disorders

Cited by 11