Tackling the widespread and critical impact of batch effects in high-throughput data
High-throughput technologies are widely used, for example to assay genetic variants, gene
and protein expression, and epigenetic modifications. One often overlooked complication …
and protein expression, and epigenetic modifications. One often overlooked complication …
Enter the matrix: factorization uncovers knowledge from omics
Omics data contain signals from the molecular, physical, and kinetic inter-and intracellular
interactions that control biological systems. Matrix factorization (MF) techniques can reveal …
interactions that control biological systems. Matrix factorization (MF) techniques can reveal …
Confronting false discoveries in single-cell differential expression
Differential expression analysis in single-cell transcriptomics enables the dissection of cell-
type-specific responses to perturbations such as disease, trauma, or experimental …
type-specific responses to perturbations such as disease, trauma, or experimental …
Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences
Motivation In RNA-seq differential expression analysis, investigators aim to detect those
genes with changes in expression level across conditions, despite technical and biological …
genes with changes in expression level across conditions, despite technical and biological …
Bias, robustness and scalability in single-cell differential expression analysis
C Soneson, MD Robinson - Nature methods, 2018 - nature.com
Many methods have been used to determine differential gene expression from single-cell
RNA (scRNA)-seq data. We evaluated 36 approaches using experimental and synthetic …
RNA (scRNA)-seq data. We evaluated 36 approaches using experimental and synthetic …
Harmonization of multi-site diffusion tensor imaging data
Diffusion tensor imaging (DTI) is a well-established magnetic resonance imaging (MRI)
technique used for studying microstructural changes in the white matter. As with many other …
technique used for studying microstructural changes in the white matter. As with many other …
Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry
Quantitative proteomics employing mass spectrometry is an indispensable tool in life
science research. Targeted proteomics has emerged as a powerful approach for …
science research. Targeted proteomics has emerged as a powerful approach for …
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
In comparative high-throughput sequencing assays, a fundamental task is the analysis of
count data, such as read counts per gene in RNA-seq, for evidence of systematic changes …
count data, such as read counts per gene in RNA-seq, for evidence of systematic changes …
Functional normalization of 450k methylation array data improves replication in large cancer studies
We propose an extension to quantile normalization that removes unwanted technical
variation using control probes. We adapt our algorithm, functional normalization, to the …
variation using control probes. We adapt our algorithm, functional normalization, to the …
Variance component model to account for sample structure in genome-wide association studies
Although genome-wide association studies (GWASs) have identified numerous loci
associated with complex traits, imprecise modeling of the genetic relatedness within study …
associated with complex traits, imprecise modeling of the genetic relatedness within study …