Expression and Quantification

A sensitive approach to quantitative analysis of transcriptional regulation in diploid organisms is analysis of allelic imbalance (AI) in RNA sequencing..

Quantification of isoform abundance has been extensively studied at the mature-RNA level using RNA-seq but not at the level of precursor RNAs using nascent RNA sequencing. Researchers from Cold...

Single cell RNA sequencing (scRNA-seq) is a powerful tool in detailing the cellular landscape within complex tissues. Large-scale single cell transcriptomics provide both opportunities and challenges...

RNA modifications, such as N6-methyladenosine (m6A), modulate functions of cellular RNA species. However, quantifying differences in RNA...

Single-cell RNA sequencing (scRNA-seq) has enabled the unbiased, high-throughput quantification of gene expression specific to cell types and states. With...

Elucidation of cell subpopulations at high resolution is a key and challenging goal of single-cell ribonucleic acid (RNA) sequencing (scRNA-seq)...

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-sample comparisons and for...

Computational workflows for RNA sequencing data often include differential expression and functional interpretation analyses, and a number of specialized and established tools exist for performing these tasks, each generating a set of intermediate processed data and results. In order to ...

The ability to discover new cell populations by unsupervised clustering of single-cell transcriptomics data has revolutionized biology. However, all unsupervised methods have adjustable parameters, which renders it difficult for researchers to decide on the right resolution for clustering. Often it ...

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 ...