RNA-seq differential expression studies: more sequence or more replication?

Y Liu, J Zhou, KP White - Bioinformatics, 2014 - academic.oup.com
Motivation: RNA-seq is replacing microarrays as the primary tool for gene expression
studies. Many RNA-seq studies have used insufficient biological replicates, resulting in low …

Processing and analysis of RNA-seq data from public resources

Y Zoabi, N Shomron - Deep Sequencing Data Analysis, 2021 - Springer
Advances in next generation sequencing (NGS) technologies resulted in a broad array of
large-scale gene expression studies and an unprecedented volume of whole messenger …

A flexible cross-platform single-cell data processing pipeline

K Battenberg, ST Kelly, RA Ras… - Nature …, 2022 - nature.com
Single-cell RNA-sequencing analysis to quantify the RNA molecules in individual cells has
become popular, as it can obtain a large amount of information from each experiment. We …

ascend: R package for analysis of single-cell RNA-seq data

A Senabouth, SW Lukowski, JA Hernandez… - …, 2019 - academic.oup.com
Background Recent developments in single-cell RNA sequencing (scRNA-seq) platforms
have vastly increased the number of cells typically assayed in an experiment. Analysis of …

Vespucci: a system for building annotated databases of nascent transcripts

KA Allison, MU Kaikkonen, T Gaasterland… - Nucleic acids …, 2014 - academic.oup.com
Global run-on sequencing (GRO-seq) is a recent addition to the series of high-throughput
sequencing methods that enables new insights into transcriptional dynamics within a cell …

CLEAR: coverage-based limiting-cell experiment analysis for RNA-seq

LA Walker, MG Sovic, CL Chiang, E Hu… - Journal of translational …, 2020 - Springer
Background Direct cDNA preamplification protocols developed for single-cell RNA-seq have
enabled transcriptome profiling of precious clinical samples and rare cell populations …

RNA-seq: from technology to biology

S Marguerat, J Bähler - Cellular and molecular life sciences, 2010 - Springer
Next-generation sequencing technologies are now being exploited not only to analyse static
genomes, but also dynamic transcriptomes in an approach termed RNA-seq. Although these …

RNA-Seq analysis: methods, applications and challenges

F Geraci, I Saha, M Bianchini - Frontiers in Genetics, 2020 - frontiersin.org
RNA-seq has revolutionized the research community approach to studying gene expression.
In fact, this technology has opened up the possibility of quantifying the expression level of all …

The devil in the details of RNA-seq

A Kratz, P Carninci - Nature biotechnology, 2014 - nature.com
The devil in the details of RNA-seq | Nature Biotechnology Skip to main content Thank you for
visiting nature.com. You are using a browser version with limited support for CSS. To obtain the …

RNA sequencing data: hitchhiker's guide to expression analysis

K Van den Berge, KM Hembach… - Annual Review of …, 2019 - annualreviews.org
Gene expression is the fundamental level at which the results of various genetic and
regulatory programs are observable. The measurement of transcriptome-wide gene …