The triumphs and limitations of computational methods for scRNA-seq

PV Kharchenko - Nature methods, 2021 - nature.com
The rapid progress of protocols for sequencing single-cell transcriptomes over the past
decade has been accompanied by equally impressive advances in the computational …

Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data

TS Andrews, VY Kiselev, D McCarthy, M Hemberg - Nature protocols, 2021 - nature.com
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 …

[HTML][HTML] Single-cell RNA-seq technologies and related computational data analysis

G Chen, B Ning, T Shi - Frontiers in genetics, 2019 - frontiersin.org
Single-cell RNA sequencing (scRNA-seq) technologies allow the dissection of gene
expression at single-cell resolution, which greatly revolutionizes transcriptomic studies. A …

[HTML][HTML] Design and computational analysis of single-cell RNA-sequencing experiments

R Bacher, C Kendziorski - Genome biology, 2016 - Springer
Single-cell RNA-sequencing (scRNA-seq) has emerged as a revolutionary tool that allows
us to address scientific questions that eluded examination just a few years ago. With the …

[HTML][HTML] Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database

L Zappia, B Phipson, A Oshlack - PLoS computational biology, 2018 - journals.plos.org
As single-cell RNA-sequencing (scRNA-seq) datasets have become more widespread the
number of tools designed to analyse these data has dramatically increased. Navigating the …

[HTML][HTML] A systematic evaluation of single cell RNA-seq analysis pipelines

B Vieth, S Parekh, C Ziegenhain, W Enard… - Nature …, 2019 - nature.com
The recent rapid spread of single cell RNA sequencing (scRNA-seq) methods has created a
large variety of experimental and computational pipelines for which best practices have not …

Introduction to single‐cell RNA sequencing

TK Olsen, N Baryawno - Current protocols in molecular biology, 2018 - Wiley Online Library
During the last decade, high‐throughput sequencing methods have revolutionized the entire
field of biology. The opportunity to study entire transcriptomes in great detail using RNA …

Critical downstream analysis steps for single-cell RNA sequencing data

Z Zhang, F Cui, C Lin, L Zhao, C Wang… - Briefings in …, 2021 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) has enabled us to study biological questions at
the single-cell level. Currently, many analysis tools are available to better utilize these …

Single-cell RNA sequencing analysis: a step-by-step overview

S Slovin, A Carissimo, F Panariello, A Grimaldi… - RNA …, 2021 - Springer
Thanks to innovative sample-preparation and sequencing technologies, gene expression in
individual cells can now be measured for thousands of cells in a single experiment. Since its …

[HTML][HTML] Over 1000 tools reveal trends in the single-cell RNA-seq analysis landscape

L Zappia, FJ Theis - Genome biology, 2021 - Springer
Recent years have seen a revolution in single-cell RNA-sequencing (scRNA-seq)
technologies, datasets, and analysis methods. Since 2016, the scRNA-tools database has …