Single‐cell RNA‐seq has enabled gene expression to be studied at an unprecedented
resolution. The promise of this technology is attracting a growing user base for single‐cell …

Rapid progress in the development of next-generation sequencing (NGS) technologies in
recent years has provided many valuable insights into complex biological systems, ranging …

The simultaneous measurement of multiple modalities represents an exciting frontier for
single-cell genomics and necessitates computational methods that can define cellular states …

INTRODUCTION Cancer immunotherapies that target tumor-specific T cells have benefited
many cancer patients, but the clinical efficacy varies greatly among different cancer types …

Scanpy is a scalable toolkit for analyzing single-cell gene expression data. It includes
methods for preprocessing, visualization, clustering, pseudotime and trajectory inference …

RNA velocity has opened up new ways of studying cellular differentiation in single-cell RNA-
sequencing data. It describes the rate of gene expression change for an individual gene at a …

RNA abundance is a powerful indicator of the state of individual cells. Single-cell RNA
sequencing can reveal RNA abundance with high quantitative accuracy, sensitivity and …

Single-cell trajectories can unveil how gene regulation governs cell fate decisions. However,
learning the structure of complex trajectories with multiple branches remains a challenging …

Gastrulation is the fundamental process in all multicellular animals through which the basic
body plan is first laid down,,–. It is pivotal in generating cellular diversity coordinated with …

The recent boom in microfluidics and combinatorial indexing strategies, combined with low
sequencing costs, has empowered single-cell sequencing technology. Thousands—or even …