Expression and Quantification

In current statistical methods for calling differentially expressed genes in RNA-Seq experiments, the assumption is that an adjusted observed gene count represents an unknown true gene count...

University of Montpellier researchers have developed a k-mer-based computational protocol, DE-kupl, for capturing local RNA variation in a set of RNA-seq...

The correct identification of differentially expressed genes (DEGs) between specific conditions is a key in the understanding phenotypic variation. High...

Transposable elements (TEs) are DNA sequences which are capable of moving from one location to another and represent a large proportion (45%) of the human genome. TEs have functional roles in a variety of biological phenomena such as cancer, neurodegenerative ...

Iowa State University researchers propose a novel method and software tool, Strawberry, for transcript reconstruction and quantification from RNA-Seq data under the guidance of genome alignment and...

Cell types in cell populations change as the condition changes: some cell types die out, new cell types may emerge and surviving cell types evolve to adapt to the new condition. Using single-cell RNA-sequencing data that measure the gene expression ...

Next generation sequencing allows the identification of genes consisting of differentially expressed transcripts, a term which usually refers to changes in the overall expression level. A specific type of differential expression is differential transcript usage (DTU) and targets changes in ...

Motivated by the lack of easily implementable and generally applicable strategies to increase and assess data accuracy, researchers from the University of Georgia devised a novel label-free approach, termed REQUIEM, to address challenges in relative quantitation. For comparing the relative ...

Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes in RNA-seq data. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and ...

RNA sequencing (RNA-seq) is a high throughput technology that profiles gene expression in a genome-wide manner. RNA-seq has been mainly used for testing differential expression (DE) of transcripts between two conditions and has recently been used for testing differential alternative ...