Expression and Quantification

Most existing dimensionality reduction and clustering packages for single-cell RNA-Seq (scRNA-Seq) data deal with dropouts by heavy modelling and computational machinery. Here researchers from the Victor Chang Cardiac Research Institute introduce CIDR (Clustering through Imputation and Dimensionality Reduction), an ultrafast ...

The temporal and spatial-specific expression pattern of a transcript in multiple tissues and cell types can indicate key clues about its function. While several gene atlas available online as pre-computed databases for known gene models, it’s still challenging to obtain ...

Single-cell gene expression studies promise to reveal rare cell types and cryptic states, but the high variability of single-cell RNA-seq measurements frustrates efforts to assay transcriptional differences between cells. University of Washington researchers have developed the Census algorithm to convert ...

The development of single-cell RNA-seq has allowed the detection of gene expression at an anatomical resolution that is not accessible by bulk RNA-seq approaches. While single-cell RNA-seq methods have been successfully used to identify new cell types in complex tissues, ...

Next-generation sequencing technologies have made RNA sequencing (RNA-seq) a popular choice for measuring gene expression level. To reduce the noise of gene expression measures and compare them between several conditions or samples, normalization is an essential step to adjust for ...

Pseudotime analyses of single-cell RNA-seq data have become increasingly common. Typically, a latent trajectory corresponding to a biological process of interest – such as differentiation or cell cycle – is discovered. However, relatively little attention has been paid to modelling ...

Researchers at Oregon State University examined RNA-Seq data on 211 biological samples from 24 different Arabidopsis experiments carried out by different labs. They grouped the samples according to tissue types, and in each of the groups, they identified genes that ...

As part of the process of preparing scRNA-seq libraries, a diverse template is typically amplified by PCR. During amplification, spurious chimeric molecules can be formed between molecules originating in different cells. While several computational and experimental strategies have been suggested ...

Over recent decades, substantial efforts have been made to understand the interactions between host genomes and transposable elements (TEs). The impact of TEs on the regulation of host genes is well known, with TEs acting as platforms of regulatory sequences. ...

RNA-seq experiments are usually carried out in three or fewer replicates. In order to work well with so few samples, Differential Gene Expression (DGE) tools typically assume the form of the underlying distribution of gene expression. A recent highly replicated ...