CLASS2: accurate and efficient splice variant annotation from RNA-seq reads
Next generation sequencing of cellular RNA is making it possible to characterize genes and
alternative splicing in unprecedented detail. However, designing bioinformatics tools to …
alternative splicing in unprecedented detail. However, designing bioinformatics tools to …
Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data
Transcript quantification is a long-standing problem in genomics and estimating the relative
abundance of alternatively-spliced isoforms from the same transcript is an important special …
abundance of alternatively-spliced isoforms from the same transcript is an important special …
Towards reliable isoform quantification using RNA-SEQ data
Background In eukaryotes, alternative splicing often generates multiple splice variants from
a single gene. Here weexplore the use of RNA sequencing (RNA-Seq) datasets to address …
a single gene. Here weexplore the use of RNA sequencing (RNA-Seq) datasets to address …
Quantitative visualization of alternative exon expression from RNA-seq data
Y Katz, ET Wang, J Silterra, S Schwartz, B Wong… - …, 2015 - academic.oup.com
Motivation: Analysis of RNA sequencing (RNA-Seq) data revealed that the vast majority of
human genes express multiple mRNA isoforms, produced by alternative pre-mRNA splicing …
human genes express multiple mRNA isoforms, produced by alternative pre-mRNA splicing …
Evaluation and comparison of computational tools for RNA-seq isoform quantification
Background Alternatively spliced transcript isoforms are commonly observed in higher
eukaryotes. The expression levels of these isoforms are key for understanding normal …
eukaryotes. The expression levels of these isoforms are key for understanding normal …
Separating measurement and expression models clarifies confusion in single cell RNA-seq analysis
A Sarkar, M Stephens - BioRxiv, 2020 - biorxiv.org
How to model and analyze scRNA-seq data has been the subject of considerable confusion
and debate. The high proportion of zero counts in a typical scRNA-seq data matrix has …
and debate. The high proportion of zero counts in a typical scRNA-seq data matrix has …
[HTML][HTML] satuRn: Scalable analysis of differential transcript usage for bulk and single-cell RNA-sequencing applications
Alternative splicing produces multiple functional transcripts from a single gene.
Dysregulation of splicing is known to be associated with disease and as a hallmark of …
Dysregulation of splicing is known to be associated with disease and as a hallmark of …
Power analysis of single-cell RNA-sequencing experiments
Single-cell RNA sequencing (scRNA-seq) has become an established and powerful method
to investigate transcriptomic cell-to-cell variation, thereby revealing new cell types and …
to investigate transcriptomic cell-to-cell variation, thereby revealing new cell types and …
rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data
Ultra-deep RNA sequencing (RNA-Seq) has become a powerful approach for genome-wide
analysis of pre-mRNA alternative splicing. We previously developed multivariate analysis of …
analysis of pre-mRNA alternative splicing. We previously developed multivariate analysis of …
A survey of software for genome-wide discovery of differential splicing in RNA-Seq data
JE Hooper - Human genomics, 2014 - Springer
Alternative splicing is a major contributor to cellular diversity. Therefore the identification and
quantification of differentially spliced transcripts in genome-wide transcript analysis is an …
quantification of differentially spliced transcripts in genome-wide transcript analysis is an …