Motivation: RNA-seq co-expression analysis is in its infancy and reasonable practices remain
poorly defined. We assessed a variety of RNA-seq expression data to determine factors …

Single-cell RNA-sequencing (scRNA-seq) technology provides a new avenue to discover
and characterize cell types; however, the experiment-specific technical biases and analytic …

The use of the human reference genome has shaped methods and data across modern
genomics. This has offered many benefits while creating a few constraints. In the following …

Differential expression (DE) is commonly used to explore molecular mechanisms of biological
conditions. While many studies report significant results between their groups of interest, …

Evaluating gene networks with respect to known biology is a common task but often a
computationally costly one. Many computational experiments are difficult to apply exhaustively in …

Background Co-expression networks have been a useful tool for functional genomics,
providing important clues about the cellular and biochemical mechanisms that are active in …

Networks constructed from aggregated protein–protein interaction data are commonplace in
biology. But the studies these data are derived from were conducted with their own …

X-chromosome inactivation (XCI) is a random, permanent, and developmentally early
epigenetic event that occurs during mammalian embryogenesis. We harness these features to …

Co-expression analysis has provided insight into gene function in organisms from Arabidopsis
to zebrafish. Comparison across species has the potential to enrich these results, for …

Genes encoding proteins in a common pathway are often found near each other along bacterial
chromosomes. Several explanations have been proposed to account for the evolution of …