Single-cell RNA-seq with spike-in cells enables accurate quantification of cell-specific drug effects in pancreatic islets

B Marquina-Sanchez, N Fortelny, M Farlik, A Vieira… - Genome biology, 2020 - Springer
Background Single-cell RNA-seq (scRNA-seq) is emerging as a powerful tool to dissect cell-
specific effects of drug treatment in complex tissues. This application requires high levels of …

Multiplexed single-cell RNA-seq via transient barcoding for simultaneous expression profiling of various drug perturbations

D Shin, W Lee, JH Lee, D Bang - Science advances, 2019 - science.org
The development of high-throughput single-cell RNA sequencing (scRNA-seq) has enabled
access to information about gene expression in individual cells and insights into new …

Single-nucleus RNA sequencing of human pancreatic islets identifies novel gene sets and distinguishes β-cell subpopulations with dynamic transcriptome profiles

RB Kang, Y Li, C Rosselot, T Zhang, M Siddiq… - Genome Medicine, 2023 - Springer
Background Single-cell RNA sequencing (scRNA-seq) provides valuable insights into
human islet cell types and their corresponding stable gene expression profiles. However …

bigSCale: an analytical framework for big-scale single-cell data

G Iacono, E Mereu, A Guillaumet-Adkins… - Genome …, 2018 - genome.cshlp.org
Single-cell RNA sequencing (scRNA-seq) has significantly deepened our insights into
complex tissues, with the latest techniques capable of processing tens of thousands of cells …

Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists

X Zhu, TK Wolfgruber, A Tasato, C Arisdakessian… - Genome medicine, 2017 - Springer
Background Single-cell RNA sequencing (scRNA-Seq) is an increasingly popular platform
to study heterogeneity at the single-cell level. Computational methods to process scRNA …

Integrating single-cell transcriptomic data across different conditions, technologies, and species

A Butler, P Hoffman, P Smibert, E Papalexi… - Nature …, 2018 - nature.com
Computational single-cell RNA-seq (scRNA-seq) methods have been successfully applied
to experiments representing a single condition, technology, or species to discover and …

scGEAToolbox: a Matlab toolbox for single-cell RNA sequencing data analysis

JJ Cai - 2020 - academic.oup.com
Motivation Single-cell RNA sequencing (scRNA-seq) technology has revolutionized the way
research is done in biomedical sciences. It provides an unprecedented level of resolution …

Profiling of single‐cell transcriptomes

W Chen, V Gardeux, A Meireles‐Filho… - Current protocols in …, 2017 - Wiley Online Library
Complex biological systems are composed of multiple cell types whose transcriptional
activity can vary due to differences in cell state, environmental stimulation, or intrinsic …

Case-control analysis of single-cell RNA-seq studies

V Petukhov, A Igolkina, R Rydbirk, S Mei… - bioRxiv, 2022 - biorxiv.org
Single-cell RNA-seq (scRNA-seq) assays are being increasingly utilized to investigate
specific hypotheses in both basic biology and clinically-applied studies. The design of most …

ASAP: a web-based platform for the analysis and interactive visualization of single-cell RNA-seq data

V Gardeux, FPA David, A Shajkofci, PC Schwalie… - …, 2017 - academic.oup.com
Motivation Single-cell RNA-sequencing (scRNA-seq) allows whole transcriptome profiling of
thousands of individual cells, enabling the molecular exploration of tissues at the cellular …