Comparative analysis of sequencing technologies for single-cell transcriptomics

KN Natarajan, Z Miao, M Jiang, X Huang, H Zhou, J Xie… - Genome Biology, 2019 - Springer
Single-cell RNA-seq technologies require library preparation prior to sequencing. Here, we
present the first report to compare the cheaper BGISEQ-500 platform to the Illumina HiSeq …

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 …

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 …

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 …

scRNA‐seq data analysis method to improve analysis performance

J Lu, Y Sheng, W Qian, M Pan, X Zhao… - IET …, 2023 - Wiley Online Library
With the development of single‐cell RNA sequencing technology (scRNA‐seq), we have the
ability to study biological questions at the level of the individual cell transcriptome …

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 …

Using neural networks for reducing the dimensions of single-cell RNA-Seq data

C Lin, S Jain, H Kim, Z Bar-Joseph - Nucleic acids research, 2017 - academic.oup.com
While only recently developed, the ability to profile expression data in single cells (scRNA-
Seq) has already led to several important studies and findings. However, this technology …

A comprehensive survey of statistical approaches for differential expression analysis in single-cell RNA sequencing studies

S Das, A Rai, ML Merchant, MC Cave, SN Rai - Genes, 2021 - mdpi.com
Single-cell RNA-sequencing (scRNA-seq) is a recent high-throughput sequencing
technique for studying gene expressions at the cell level. Differential Expression (DE) …

[HTML][HTML] Single-cell transcriptomics bioinformatics and computational challenges

OB Poirion, X Zhu, T Ching, L Garmire - Frontiers in genetics, 2016 - frontiersin.org
The emerging single-cell RNA-Seq (scRNA-Seq) technology holds the promise to
revolutionize our understanding of diseases and associated biological processes at an …