It is a basic task in high-throughput gene expression profiling studies to identify differentially
expressed genes (DEGs) between two phenotypes. But the weakly differential expression …

Motivation For some specific tissues, such as the heart and brain, normal controls are
difficult to obtain. Thus, studies with only a particular type of disease samples (one …

Motivation: The differential expression analysis focusing on inter-group comparison can
capture only differentially expressed genes (DE genes) at the population level, which may …

The highly stable within-sample relative expression orderings (REOs) of gene pairs in a
particular type of human normal tissue are widely reversed in the cancer condition. Based …

Due to the invasiveness nature of tissue biopsy, it is common that investigators cannot
collect sufficient normal controls for comparison with diseased samples. We developed a …

To detect differentially expressed genes (DEGs) in small-scale cell line experiments, usually
with only two or three technical replicates for each state, the commonly used statistical …

Identification of individual-level differentially expressed genes (DEGs) is a pre-step for the
analysis of disease-specific biological mechanisms and precision medicine. Previous …

Motivation: Tests of differentially expressed genes (DEGs) from microarray experiments are
based on the null hypothesis that genes that are irrelevant to the phenotype/stimulus are …

Motivation Detecting differentially expressed (DE) genes between disease and normal
control group is one of the most common analyses in genome-wide transcriptomic data …

Background Differential co-expression analysis, as a complement of differential expression
analysis, offers significant insights into the changes in molecular mechanism of different …