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[PDF][PDF] edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets
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 …
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
Over the past few decades, RNA sequencing has significantly progressed, becoming a
paramount approach for transcriptome profiling. The revolution from bulk RNA sequencing …
paramount approach for transcriptome profiling. The revolution from bulk RNA sequencing …
RNA sequencing: the teenage years
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 …
transcriptome-wide analysis of differential gene expression and differential splicing of …
Cell–cell communication: new insights and clinical implications
Multicellular organisms are composed of diverse cell types that must coordinate their
behaviors through communication. Cell–cell communication (CCC) is essential for growth …
behaviors through communication. Cell–cell communication (CCC) is essential for growth …
Nanopore native RNA sequencing of a human poly (A) transcriptome
High-throughput complementary DNA sequencing technologies have advanced our
understanding of transcriptome complexity and regulation. However, these methods lose …
understanding of transcriptome complexity and regulation. However, these methods lose …
EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data
Droplet-based single-cell RNA sequencing protocols have dramatically increased the
throughput of single-cell transcriptomics studies. A key computational challenge when …
throughput of single-cell transcriptomics studies. A key computational challenge when …
RNA-Seq differential expression analysis: An extended review and a software tool
The correct identification of differentially expressed genes (DEGs) between specific
conditions is a key in the understanding phenotypic variation. High-throughput transcriptome …
conditions is a key in the understanding phenotypic variation. High-throughput transcriptome …
Massive mining of publicly available RNA-seq data from human and mouse
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 …
quantification. However, publicly available RNA-seq data is currently provided mostly in raw …
Near-optimal probabilistic RNA-seq quantification
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 …
faster than previous approaches and achieves similar accuracy. Kallisto pseudoaligns reads …
[HTML][HTML] The technology and biology of single-cell RNA sequencing
The differences between individual cells can have profound functional consequences, in
both unicellular and multicellular organisms. Recently developed single-cell mRNA …
both unicellular and multicellular organisms. Recently developed single-cell mRNA …