SpliceTrap: a method to quantify alternative splicing under single cellular conditions
Motivation: Alternative splicing (AS) is a pre-mRNA maturation process leading to the
expression of multiple mRNA variants from the same primary transcript. More than 90% of …
expression of multiple mRNA variants from the same primary transcript. More than 90% of …
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 …
rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data
Pre-mRNA alternative splicing is a prevalent mechanism for diversifying eukaryotic
transcriptomes and proteomes. Regulated alternative splicing plays a role in many …
transcriptomes and proteomes. Regulated alternative splicing plays a role in many …
SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts
MC Ryan, J Cleland, RG Kim, WC Wong… - …, 2012 - academic.oup.com
SpliceSeq is a resource for RNA-Seq data that provides a clear view of alternative splicing
and identifies potential functional changes that result from splice variation. It displays …
and identifies potential functional changes that result from splice variation. It displays …
Complementarity of assembly-first and mapping-first approaches for alternative splicing annotation and differential analysis from RNAseq data
Genome-wide analyses estimate that more than 90% of multi exonic human genes produce
at least two transcripts through alternative splicing (AS). Various bioinformatics methods are …
at least two transcripts through alternative splicing (AS). Various bioinformatics methods are …
Alternative splicing signatures in RNA‐seq data: percent spliced in (PSI)
Thousands of alternative exons are spliced out of messenger RNA to increase protein
diversity. High‐throughput sequencing of short cDNA fragments (RNA‐seq) generates a …
diversity. High‐throughput sequencing of short cDNA fragments (RNA‐seq) generates a …
Leveraging transcript quantification for fast computation of alternative splicing profiles
GP Alamancos, A Pagès, JL Trincado, N Bellora… - Rna, 2015 - rnajournal.cshlp.org
Alternative splicing plays an essential role in many cellular processes and bears major
relevance in the understanding of multiple diseases, including cancer. High-throughput RNA …
relevance in the understanding of multiple diseases, including cancer. High-throughput RNA …
[HTML][HTML] Alternative splicing: Human disease and quantitative analysis from high-throughput sequencing
Alternative splicing contributes to the majority of protein diversity in higher eukaryotes by
allowing one gene to generate multiple distinct protein isoforms. It adds another regulation …
allowing one gene to generate multiple distinct protein isoforms. It adds another regulation …
MAJIQ-SPEL: web-tool to interrogate classical and complex splicing variations from RNA-Seq data
CJ Green, MR Gazzara, Y Barash - Bioinformatics, 2018 - academic.oup.com
Analysis of RNA sequencing (RNA-Seq) data have highlighted the fact that most genes
undergo alternative splicing (AS) and that these patterns are tightly regulated. Many of these …
undergo alternative splicing (AS) and that these patterns are tightly regulated. Many of these …
ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events
Background While the reconstruction of transcripts from a sample of RNA-Seq data is a
computationally expensive and complicated task, the detection of splicing events from RNA …
computationally expensive and complicated task, the detection of splicing events from RNA …