[HTML][HTML] A survey of computational methods in transcriptome-wide alternative splicing analysis

J Wang, Z Ye, THM Huang, H Shi, V Jin - Biomolecular concepts, 2015 - degruyter.com
Alternative splicing is widely recognized for its roles in regulating genes and creating gene
diversity. Consequently the identification and quantification of differentially spliced …

Selecting Differential Splicing Methods: Practical Considerations

BJ Draper, MJ Dunning, DC James - arXiv preprint arXiv:2409.05458, 2024 - arxiv.org
Alternative splicing is crucial in gene regulation, with significant implications in clinical
settings and biotechnology. This review article compiles bioinformatics RNA-seq tools for …

[HTML][HTML] Splicing Express: a software suite for alternative splicing analysis using next-generation sequencing data

JE Kroll, J Kim, L Ohno-Machado, SJ de Souza - PeerJ, 2015 - peerj.com
Motivation. Alternative splicing events (ASEs) are prevalent in the transcriptome of
eukaryotic species and are known to influence many biological phenomena. The …

[HTML][HTML] Integrative analysis of many RNA-seq datasets to study alternative splicing

W Li, C Dai, S Kang, XJ Zhou - Methods, 2014 - Elsevier
Alternative splicing is an important gene regulatory mechanism that dramatically increases
the complexity of the proteome. However, how alternative splicing is regulated and how …

[HTML][HTML] 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 …

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 …

A comprehensive benchmarking of differential splicing tools for RNA-seq analysis at the event level

M Jiang, S Zhang, H Yin, Z Zhuo… - Briefings in …, 2023 - academic.oup.com
RNA alternative splicing, a post-transcriptional stage in eukaryotes, is crucial in cellular
homeostasis and disease processes. Due to the rapid development of the next-generation …

[HTML][HTML] Detection, annotation and visualization of alternative splicing from RNA-Seq data with SplicingViewer

Q Liu, C Chen, E Shen, F Zhao, Z Sun, J Wu - Genomics, 2012 - Elsevier
Alternative splicing is a crucial mechanism by which diverse gene products can be
generated from a limited number of genes, and is thought to be involved in complex …

ASpli: integrative analysis of splicing landscapes through RNA-Seq assays

E Mancini, A Rabinovich, J Iserte, M Yanovsky… - …, 2021 - academic.oup.com
Motivation Genome-wide analysis of alternative splicing has been a very active field of
research since the early days of next generation sequencing technologies. Since then, ever …

rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data

Y Wang, Z Xie, E Kutschera, JI Adams… - Nature …, 2024 - nature.com
Pre-mRNA alternative splicing is a prevalent mechanism for diversifying eukaryotic
transcriptomes and proteomes. Regulated alternative splicing plays a role in many …