Computational and analytical challenges in single-cell transcriptomics

O Stegle, SA Teichmann, JC Marioni - Nature Reviews Genetics, 2015 - nature.com
The development of high-throughput RNA sequencing (RNA-seq) at the single-cell level has
already led to profound new discoveries in biology, ranging from the identification of novel …

Cerebro: interactive visualization of scRNA-seq data

R Hillje, PG Pelicci, L Luzi - Bioinformatics, 2020 - academic.oup.com
Despite the growing availability of sophisticated bioinformatic methods for the analysis of
single-cell RNA-seq data, few tools exist that allow biologists without extensive bioinformatic …

SigEMD: A powerful method for differential gene expression analysis in single-cell RNA sequencing data

T Wang, S Nabavi - Methods, 2018 - Elsevier
Differential gene expression analysis is one of the significant efforts in single cell RNA
sequencing (scRNAseq) analysis to discover the specific changes in expression 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 …

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

L Haghverdi, ATL Lun, MD Morgan, JC Marioni - Nature biotechnology, 2018 - nature.com
Large-scale single-cell RNA sequencing (scRNA-seq) data sets that are produced in
different laboratories and at different times contain batch effects that may compromise the …

Machine learning and statistical methods for clustering single-cell RNA-sequencing data

R Petegrosso, Z Li, R Kuang - Briefings in bioinformatics, 2020 - academic.oup.com
Single-cell RNAsequencing (scRNA-seq) technologies have enabled the large-scale whole-
transcriptome profiling of each individual single cell in a cell population. A core analysis of …

Systematic comparative analysis of single cell RNA-sequencing methods

J Ding, X Adiconis, SK Simmons, MS Kowalczyk… - BioRxiv, 2019 - biorxiv.org
ABSTRACT A multitude of single-cell RNA sequencing methods have been developed in
recent years, with dramatic advances in scale and power, and enabling major discoveries …

How to design a single-cell RNA-sequencing experiment: pitfalls, challenges and perspectives

A Dal Molin, B Di Camillo - Briefings in bioinformatics, 2019 - academic.oup.com
The sequencing of the transcriptome of single cells, or single-cell RNA-sequencing, has now
become the dominant technology for the identification of novel cell types in heterogeneous …

Computational approaches for interpreting sc RNA‐seq data

R Rostom, V Svensson, SA Teichmann, G Kar - FEBS letters, 2017 - Wiley Online Library
The recent developments in high‐throughput single‐cell RNA sequencing technology (sc
RNA‐seq) have enabled the generation of vast amounts of transcriptomic data at cellular …

[HTML][HTML] Comparison and evaluation of statistical error models for scRNA-seq

S Choudhary, R Satija - Genome biology, 2022 - Springer
Background Heterogeneity in single-cell RNA-seq (scRNA-seq) data is driven by multiple
sources, including biological variation in cellular state as well as technical variation …