[PDF][PDF] edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets

Y Chen, L Chen, ATL Lun, PL Baldoni… - Nucleic Acids …, 2025‏ - academic.oup.com
Abstract edgeR is an R/Bioconductor software package for differential analyses of
sequencing data in the form of read counts for genes or genomic features. Over the past 15 …

RNA sequencing: new technologies and applications in cancer research

M Hong, S Tao, L Zhang, LT Diao, X Huang… - Journal of hematology & …, 2020‏ - Springer
Over the past few decades, RNA sequencing has significantly progressed, becoming a
paramount approach for transcriptome profiling. The revolution from bulk RNA sequencing …

RNA sequencing: the teenage years

R Stark, M Grzelak, J Hadfield - Nature Reviews Genetics, 2019‏ - nature.com
Over the past decade, RNA sequencing (RNA-seq) has become an indispensable tool for
transcriptome-wide analysis of differential gene expression and differential splicing of …

Cell–cell communication: new insights and clinical implications

J Su, Y Song, Z Zhu, X Huang, J Fan, J Qiao… - Signal Transduction and …, 2024‏ - nature.com
Multicellular organisms are composed of diverse cell types that must coordinate their
behaviors through communication. Cell–cell communication (CCC) is essential for growth …

Nanopore native RNA sequencing of a human poly (A) transcriptome

RE Workman, AD Tang, PS Tang, M Jain, JR Tyson… - Nature …, 2019‏ - nature.com
High-throughput complementary DNA sequencing technologies have advanced our
understanding of transcriptome complexity and regulation. However, these methods lose …

EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data

ATL Lun, S Riesenfeld, T Andrews, TP Dao, T Gomes… - Genome biology, 2019‏ - Springer
Droplet-based single-cell RNA sequencing protocols have dramatically increased the
throughput of single-cell transcriptomics studies. A key computational challenge when …

RNA-Seq differential expression analysis: An extended review and a software tool

J Costa-Silva, D Domingues, FM Lopes - PloS one, 2017‏ - journals.plos.org
The correct identification of differentially expressed genes (DEGs) between specific
conditions is a key in the understanding phenotypic variation. High-throughput transcriptome …

Massive mining of publicly available RNA-seq data from human and mouse

A Lachmann, D Torre, AB Keenan, KM Jagodnik… - Nature …, 2018‏ - nature.com
RNA sequencing (RNA-seq) is the leading technology for genome-wide transcript
quantification. However, publicly available RNA-seq data is currently provided mostly in raw …

Near-optimal probabilistic RNA-seq quantification

NL Bray, H Pimentel, P Melsted, L Pachter - Nature biotechnology, 2016‏ - nature.com
We present kallisto, an RNA-seq quantification program that is two orders of magnitude
faster than previous approaches and achieves similar accuracy. Kallisto pseudoaligns reads …

[HTML][HTML] The technology and biology of single-cell RNA sequencing

AA Kolodziejczyk, JK Kim, V Svensson, JC Marioni… - Molecular cell, 2015‏ - cell.com
The differences between individual cells can have profound functional consequences, in
both unicellular and multicellular organisms. Recently developed single-cell mRNA …