Expression and Quantification

RNA sequencing (RNA-seq) is a common and widespread biological assay, and an increasing amount of data is generated with it. In practice, there are a large number of individual steps a researcher must perform before raw RNA-seq reads yield directly ...

Despite substantial progress in single-cell RNA-seq (scRNA-seq) data analysis methods, there is still little agreement on how to best normalize such data...

Alternative RNA isoforms are defined by promoter choice, alternative splicing, and polyA site selection. Although differential isoform expression is known to play a large regulatory role in eukaryotes, it has proved challenging to study with standard short-read RNA-seq because of ...

Clustering is a critical step in single cell-based studies. Most existing methods support unsupervised clustering without the a priori exploitation of any domain knowledge. When confronted by the high dimensionality and pervasive dropout events...

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

The reproducibility of gene expression measured by RNA sequencing (RNA-Seq) is dependent on the sequencing depth. While unmapped or non-exonic reads do not contribute to gene expression quantification, duplicate reads contribute to the quantification...

RNA sequencing (RNA-seq) is widely used to identify differentially expressed genes (DEGs) and reveal biological mechanisms underlying complex biological processes. RNA-seq is often performed on...

In an effort to address a major challenge when analyzing large single-cell RNA-sequencing datasets, researchers from The University of Texas MD Anderson Cancer Center have developed a new tool...

RNA sequencing is an indispensable research tool used in a broad range of transcriptome analysis studies. The most common application of RNA...

The variation in gene expression profiles of cells captured in different phases of the cell cycle can interfere with cell type identification and functional analysis of single cell RNA-Seq (scRNA-Seq) data. Researchers from the University of Connecticut Health Center have ...