[HTML][HTML] Eleven grand challenges in single-cell data science
The recent boom in microfluidics and combinatorial indexing strategies, combined with low
sequencing costs, has empowered single-cell sequencing technology. Thousands—or even …
sequencing costs, has empowered single-cell sequencing technology. Thousands—or even …
Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data
Single-cell RNA sequencing (scRNA-seq) is a popular and powerful technology that allows
you to profile the whole transcriptome of a large number of individual cells. However, the …
you to profile the whole transcriptome of a large number of individual cells. However, the …
[HTML][HTML] Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease
In the past decade, single-cell technologies have proliferated and improved from their
technically challenging beginnings to become common laboratory methods capable of …
technically challenging beginnings to become common laboratory methods capable of …
[HTML][HTML] Statistics or biology: the zero-inflation controversy about scRNA-seq data
Researchers view vast zeros in single-cell RNA-seq data differently: some regard zeros as
biological signals representing no or low gene expression, while others regard zeros as …
biological signals representing no or low gene expression, while others regard zeros as …
[HTML][HTML] A systematic evaluation of single-cell RNA-sequencing imputation methods
Background The rapid development of single-cell RNA-sequencing (scRNA-seq)
technologies has led to the emergence of many methods for removing systematic technical …
technologies has led to the emergence of many methods for removing systematic technical …
Droplet scRNA-seq is not zero-inflated
V Svensson - Nature Biotechnology, 2020 - nature.com
To the Editor—Potential users of single-cell RNA-sequencing (scRNA-seq) 1 often
encounter a choice between highthroughput droplet-based methods and high-sensitivity …
encounter a choice between highthroughput droplet-based methods and high-sensitivity …
Separating measurement and expression models clarifies confusion in single-cell RNA sequencing analysis
A Sarkar, M Stephens - Nature genetics, 2021 - nature.com
The high proportion of zeros in typical single-cell RNA sequencing datasets has led to
widespread but inconsistent use of terminology such as dropout and missing data. Here, we …
widespread but inconsistent use of terminology such as dropout and missing data. Here, we …
Studying stochastic systems biology of the cell with single-cell genomics data
Recent experimental developments in genome-wide RNA quantification hold considerable
promise for systems biology. However, rigorously probing the biology of living cells requires …
promise for systems biology. However, rigorously probing the biology of living cells requires …
[HTML][HTML] A hitchhiker's guide to single-cell transcriptomics and data analysis pipelines
Single-cell transcriptomics (SCT) is a tour de force in the era of big omics data that has led to
the accumulation of massive cellular transcription data at an astounding resolution of single …
the accumulation of massive cellular transcription data at an astounding resolution of single …
Modelling capture efficiency of single-cell RNA-sequencing data improves inference of transcriptome-wide burst kinetics
Motivation Gene expression is characterized by stochastic bursts of transcription that occur
at brief and random periods of promoter activity. The kinetics of gene expression burstiness …
at brief and random periods of promoter activity. The kinetics of gene expression burstiness …