High-dimensional mass and flow cytometry (HDCyto) experiments have become a method
of choice for high-throughput interrogation and characterization of cell populations. Here, we …

Single-cell RNA sequencing (scRNA-seq) has become an empowering technology to
profile the transcriptomes of individual cells on a large scale. Early analyses of differential …

Ulcerative colitis and Crohn’s disease are chronic inflammatory intestinal diseases with
perplexing heterogeneity in disease manifestation and response to treatment. While the …

The advent of mass cytometry increased the number of parameters measured at the single-cell
level while decreasing the extent of crosstalk between channels relative to dye-based …

Background With the emergence of hundreds of single-cell RNA-sequencing (scRNA-seq)
datasets, the number of computational tools to analyze aspects of the generated data has …

SpatialExperiment is a new data infrastructure for storing and accessing spatially-resolved
transcriptomics data, implemented within the R/Bioconductor framework, which provides …

Mass cytometry (CyTOF) has become a method of choice for in-depth characterization of
tissue heterogeneity in health and disease, and is currently implemented in multiple clinical …

Single-cell RNA sequencing (scRNA-seq) has quickly become an empowering technology
to profile the transcriptomes of individual cells on a large scale. Many early analyses of …

A key challenge in single-cell RNA-sequencing (scRNA-seq) data analysis is batch effects
that can obscure the biological signal of interest. Although there are various tools and …

Computational methods represent the lifeblood of modern molecular biology. Benchmarking
is important for all methods, but with a focus here on computational methods, benchmarking …