Expression and Quantification

Rapid development of transcriptome sequencing technologies has resulted in a data revolution and emergence of new approaches to study transcriptomic regulation such as alternative splicing, alternative polyadenylation, CRISPR knockout...

Unsupervised clustering of single-cell RNA sequencing data (scRNA-seq) is important because it allows us to identify putative cell types. However, the large number of cells (up to millions), the high...

The random noises, sampling biases, and batch effects often confound true biological variations in single-cell RNA-sequencing (scRNA-seq) data. Adjusting such biases is key to the robust discoveries in...

The rate of raw sequence production through Next-Generation Sequencing (NGS) has been growing exponentially due to improved technology and reduced costs. This has enabled researchers to answer many biological questions through "multi-omics"...

Single-cell sequencing methods rely on molecule-counting strategies to account for amplification biases, yet no experimental strategy to evaluate counting performance exists. Researchers from...

Integrative analysis of large-scale single-cell RNA sequencing (scRNA-seq) datasets can aggregate complementary biological information from different datasets. However, most existing methods fail to efficiently integrate multiple large-scale scRNA-seq...

The standard analysis pipeline for single-cell RNA-seq data consists of sequential steps initiated by clustering the cells. An innate limitation of this pipeline is that an imperfect clustering result can irreversibly affect the succeeding steps. For example, there can be ...

Researchers at Harvard T.H. Chan School of Public Health and the University of North Carolina at Chapel Hill propose TWO-SIGMA-G, a competitive gene set...

The rise of modern gene expression profiling techniques, such as RNA-Seq, has generated a wealth of high-quality datasets spanning all fields...

The number of studies using single-cell RNA sequencing (scRNA-seq) is constantly growing. This powerful technique provides a sampling of the whole transcriptome of a cell. However, sparsity of the data can be a major hurdle when studying the...