Tag Archives: negative binomial distribution

Sample size calculation and power estimation are essential components of experimental designs in biomedical research. It is very challenging to estimate power for RNA-Seq differential expression under complex experimental designs. Moreover, the dependency among genes should be taken into account ...

RNA-sequencing (RNA-Seq) has become a preferred option to quantify gene expression, because it is more accurate and reliable than microarrays. In RNA-Seq experiments, the expression level of a gene is measured by the count of short reads that are mapped ...

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 ...

RNA-sequencing (RNA-Seq) has become a powerful technology to characterize gene expression profiles because it is more accurate and comprehensive than microarrays. Although statistical methods that have been developed for microarray data can be applied to RNA-Seq data, they are not ...

The advancement of the next-generation sequencing technology enables mapping gene expression at the single-cell level, capable of tracking cell heterogeneity and determination of cell subpopulations using single-cell RNA sequencing (scRNA-seq). Unlike the objectives of conventional RNA-seq where differential expression analysis ...

The recent advances in next generation sequencing technology have made the sequencing of RNA (i.e., RNA-Seq) an extemely popular approach for gene expression analysis. Identification of significant differential expression represents a crucial initial step in these analyses, on which most ...

Genetic and epigenetic factors contribute to the regulation of gene expression. From a statistical perspective, it makes sense to represent the expression of one gene as a response variable that changes when some covariates are altered. As a starting point, ...

Differential methylation, which concerns difference in the degree of epigenetic regulation via methylation between two conditions, has been formulated as a beta or beta-binomial distribution to address the within-group biological variability in sequencing data. However, a beta or beta-binomial model ...

A team led by researchers at the National Heart Lung and Blood Institute sequenced over 700 individuals from the Drosophila Genetic Reference Panel with the goal of identifying the optimal analysis approach for the detection of differential gene expression among ...

RNA sequencing (RNA-seq) is a powerful tool for genome-wide expression profiling of biological samples with the advantage of high-throughput and high resolution. There are many existing algorithms nowadays for quantifying expression levels and detecting differential gene expression, but none of ...