Single-cell ATAC-seq (scATAC) yields sparse data that make conventional analysis
challenging. We developed chromVAR ( http://www.github.com/GreenleafLab/chromVAR ), an R …

Human hematopoiesis involves cellular differentiation of multipotent cells into progressively
more lineage-restricted states. While the chromatin accessibility landscape of this process …

Transcription factors canonically bind nucleosome-free DNA, making the positioning of
nucleosomes within regulatory regions crucial to the regulation of gene expression. Using the …

Metastases are the main cause of cancer deaths, but the mechanisms underlying metastatic
progression remain poorly understood. We isolated pure populations of cancer cells from …

T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs),
which enables individual clones to recognize specific peptide–major histocompatibility …

Here we introduce Protein-indexed Assay of Transposase Accessible Chromatin with sequencing
(Pi-ATAC) that combines single-cell chromatin and proteomic profiling. In conjunction …

The alternative sigma factor RpoS is a central regulator of many stress responses in Escherichia
coli . The level of functional RpoS differs depending on the stress. The effect of these …

Adaptive survival requires the coordination of nutrient availability with expenditure of cellular
resources. For example, in nutrient-limited environments, 50% of all S. cerevisiae genes …

During embryonic development, a complex organism is formed from a single starting cell.
These processes of growth and differentiation are driven by large transcriptional changes, …

The iheatmapr package is an R package (Team 2000) for creating complex, interactive
heatmaps. Heatmaps are commonly used to visualize patterns in high-dimensional data, …