… We formed the normalized log-counts \(x_{ij}:=log_{2}\left (\frac {c_{ij}} {C_{j}}+1\right)\),
where C j is the number of mapped reads for sample j. We then used the row-centered matrix A …

The human immune system displays substantial variation between individuals, leading to
differences in susceptibility to autoimmune disease. We present single-cell RNA sequencing (…

Many computational methods have been developed to infer cell type proportions from bulk
transcriptomics data. However, an evaluation of the impact of data transformation, pre-…

Single-cell RNA sequencing has enabled the characterization of highly specific cell types in
many tissues, as well as both primary and stem cell-derived cell lines. An important facet of …

Data sparsity in single-cell experiments prevents an accurate assessment of gene expression
when visualized in a low-dimensional space. Here, we introduce Nebulosa, an R package …

The human leukocyte antigen (HLA) locus plays a critical role in complex traits spanning
autoimmune and infectious diseases, transplantation and cancer. While coding variation in HLA …

Motivation RNA sequencing (RNA-seq) experiments now span hundreds to thousands of
samples. Current spliced alignment software is designed to analyze each sample separately. …

Trait-associated genetic variants affect complex phenotypes primarily via regulatory mechanisms
on the transcriptome. To investigate the genetics of gene expression, we performed cis…

Children infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) develop
less severe coronavirus disease 2019 (COVID-19) than adults. The mechanisms for the …

Background Recent developments in single-cell RNA sequencing (scRNA-seq) platforms
have vastly increased the number of cells typically assayed in an experiment. Analysis of …