List of works - Davis J McCarthy

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.

scientific article

Aliskiren increases bradykinin and tissue kallikrein mRNA levels in the heart

scientific article published in September 2011

Cardelino: Integrating whole exomes and single-cell transcriptomes to reveal phenotypic impact of somatic variants

Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes

scientific article published on 16 March 2020

Choice of transcripts and software has a large effect on variant annotation

scientific article

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

scientific article published on 17 February 2016

Combined single cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity

Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity

scientific article published on 11 February 2019

Common genetic variation drives molecular heterogeneity in human iPSCs

scientific article published on 10 May 2017

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

2013 scientific article

Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates

scientific article

Differential Expression for RNA Sequencing (RNA-Seq) Data: Mapping, Summarization, Statistical Analysis, and Experimental Design

scholarly article published 22 September 2011

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

scientific article

Eleven grand challenges in single-cell data science

scientific article published on 07 February 2020

Erratum: Sequence data and association statistics from 12,940 type 2 diabetes cases and controls

scientific article published on 23 January 2018

Factors influencing success of clinical genome sequencing across a broad spectrum of disorders

scientific article

Key signaling networks are dysregulated in patients with the adipose tissue disorder, lipedema

scientific article published on 11 November 2021

MOZ and BMI1 play opposing roles during Hox gene activation in ES cells and in body segment identity specification in vivo

scientific article published on 14 April 2015

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

scientific article published on 23 March 2020

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

scientific article

Sequence data and association statistics from 12,940 type 2 diabetes cases and controls

scientific article published on 19 December 2017

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

scientific article published on 10 February 2020

Testing significance relative to a fold-change threshold is a TREAT.

scientific article

The genetic architecture of type 2 diabetes

scientific article (publication date: 11 July 2016)

Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data

scientific article published on 07 December 2020

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

scientific article published on 13 December 2019

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

scientific article (publication date: 2010)

f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq.

scientific article

List of works by Davis J McCarthy

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.

Aliskiren increases bradykinin and tissue kallikrein mRNA levels in the heart

Cardelino: Integrating whole exomes and single-cell transcriptomes to reveal phenotypic impact of somatic variants

Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes

Choice of transcripts and software has a large effect on variant annotation

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

Combined single cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity

Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity

Common genetic variation drives molecular heterogeneity in human iPSCs

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates

Differential Expression for RNA Sequencing (RNA-Seq) Data: Mapping, Summarization, Statistical Analysis, and Experimental Design

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

Eleven grand challenges in single-cell data science

Erratum: Sequence data and association statistics from 12,940 type 2 diabetes cases and controls

Factors influencing success of clinical genome sequencing across a broad spectrum of disorders

Key signaling networks are dysregulated in patients with the adipose tissue disorder, lipedema

MOZ and BMI1 play opposing roles during Hox gene activation in ES cells and in body segment identity specification in vivo

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

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

Sequence data and association statistics from 12,940 type 2 diabetes cases and controls

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

Testing significance relative to a fold-change threshold is a TREAT.

The genetic architecture of type 2 diabetes

Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data

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

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq.