Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R

DJ McCarthy, KR Campbell, ATL Lun, QF Wills - Bioinformatics, 2017 - academic.oup.com
Motivation Single-cell RNA sequencing (scRNA-seq) is increasingly used to study gene
expression at the level of individual cells. However, preparing raw sequence data for further …

Computational methods for single-cell RNA sequencing

B Hie, J Peters, SK Nyquist, AK Shalek… - Annual Review of …, 2020 - annualreviews.org
Single-cell RNA sequencing (scRNA-seq) has provided a high-dimensional catalog of
millions of cells across species and diseases. These data have spurred the development of …

A statistical simulator scDesign for rational scRNA-seq experimental design

WV Li, JJ Li - Bioinformatics, 2019 - academic.oup.com
Motivation Single-cell RNA sequencing (scRNA-seq) has revolutionized biological sciences
by revealing genome-wide gene expression levels within individual cells. However, a critical …

Single‐cell RNA sequencing technologies and applications: A brief overview

D Jovic, X Liang, H Zeng, L Lin, F Xu… - Clinical and …, 2022 - Wiley Online Library
Single‐cell RNA sequencing (scRNA‐seq) technology has become the state‐of‐the‐art
approach for unravelling the heterogeneity and complexity of RNA transcripts within …

[HTML][HTML] Reproducibility of methods to detect differentially expressed genes from single-cell RNA sequencing

T Mou, W Deng, F Gu, Y Pawitan, TN Vu - Frontiers in genetics, 2020 - frontiersin.org
Detection of differentially expressed genes is a common task in single-cell RNA-seq (scRNA-
seq) studies. Various methods based on both bulk-cell and single-cell approaches are in …

Application of deep learning on single-cell RNA sequencing data analysis: a review

M Brendel, C Su, Z Bai, H Zhang… - Genomics …, 2022 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) has become a routinely used technique to
quantify the gene expression profile of thousands of single cells simultaneously. Analysis of …

[HTML][HTML] A hitchhiker's guide to single-cell transcriptomics and data analysis pipelines

R Nayak, Y Hasija - Genomics, 2021 - Elsevier
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 …

[HTML][HTML] A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor

ATL Lun, DJ McCarthy, JC Marioni - F1000Research, 2016 - ncbi.nlm.nih.gov
Single-cell RNA sequencing (scRNA-seq) is widely used to profile the transcriptome of
individual cells. This provides biological resolution that cannot be matched by bulk RNA …

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 …

Full-length single-cell RNA sequencing with smart-seq2

S Picelli - Single Cell Methods: Sequencing and Proteomics, 2019 - Springer
In the last few years single-cell RNA sequencing (scRNA-seq) has enabled the investigation
of cellular heterogeneity at the transcriptional level, the characterization of rare cell types as …