Over the past decade, RNA sequencing (RNA-seq) has become an indispensable tool for
transcriptome-wide analysis of differential gene expression and differential splicing of …

Metagenomics and marker gene approaches, coupled with high-throughput sequencing
technologies, have revolutionized the field of microbial ecology. Metagenomics is a culture …

When identifying differentially expressed genes between two conditions using human
population RNA-seq samples, we found a phenomenon by permutation analysis: two …

Background In order to correctly decode phenotypic information from RNA-sequencing
(RNA-seq) data, careful selection of the RNA-seq quantification measure is critical for inter …

A hallmark of cancer is the avoidance of immune destruction. This process has been
primarily investigated in locally advanced or metastatic cancer,–; however, much less is …

MicrobiomeAnalyst is an easy-to-use, web-based platform for comprehensive analysis of
common data outputs generated from current microbiome studies. It enables researchers …

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 …

Pathway enrichment analysis helps researchers gain mechanistic insight into gene lists
generated from genome-scale (omics) experiments. This method identifies biological …

Trajectory inference has radically enhanced single-cell RNA-seq research by enabling the
study of dynamic changes in gene expression. Downstream of trajectory inference, it is vital …

The molecular characterization of immune subsets is important for designing effective
strategies to understand and treat diseases. We characterized 29 immune cell types within …