ArticleHuman genomics2014
A survey of software for genome-wide discovery of differential splicing in RNA-Seq data.
Article in Human genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects ofGenome research · 2024Article
- Differential splicing of neuronal genes in a Trem2*R47H mouse model mimics alterations associated with Alzheimer's disease.BMC genomics · 2023Article
- Insights into Transcriptomic Differences in Ovaries between Lambs and Adult Sheep after Superovulation Treatment.Animals : an open access journal from MDPI · 2023Article
- Maternal methionine supplementation during gestation alters alternative splicing and DNA methylation in bovine skeletal muscle.BMC genomics · 2021Article
- Alternative RNA splicing in stem cells and cancer stem cells: Importance of transcript-based expression analysis.World journal of stem cells · 2021Review
- Altered splicing associated with the pathology of inflammatory bowel disease.Human genomics · 2021Article
- Genome-wide discovery of natural variation in pre-mRNA splicing and prioritising causal alternative splicing to salt stress response in rice.The New phytologist · 2021Article
- Systematic evaluation of differential splicing tools for RNA-seq studies.Briefings in bioinformatics · 2020Article
- Revised Exon Structure of l-DOPA Decarboxylase (International journal of molecular sciences · 2020Article
- Alternative splicing is highly variable among Daphnia pulex lineages in response to acute copper exposure.BMC genomics · 2020Article
- AIDE: annotation-assisted isoform discovery with high precision.Genome research · 2019Article
- Visualization and analysis of RNA-Seq assembly graphs.Nucleic acids research · 2019Article
- Circular RNA Profiling by Illumina Sequencing via Template-Dependent Multiple Displacement Amplification.BioMed research international · 2019Article
- Environmental influences on RNA processing: Biochemical, molecular and genetic regulators of cellular response.Wiley interdisciplinary reviews. RNA · 2019Review
- Identification and Characterization of Transcripts Regulated by Circadian Alternative Polyadenylation in Mouse Liver.G3 (Bethesda, Md.) · 2018Article
- High resolution annotation of zebrafish transcriptome using long-read sequencing.Genome research · 2018Article
- PennDiff: detecting differential alternative splicing and transcription by RNA sequencing.Bioinformatics (Oxford, England) · 2018Article
- Bioinformatics challenges and perspectives when studying the effect of epigenetic modifications on alternative splicing.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Review
- Comparative Study on Alternative Splicing in Human Fungal Pathogens Suggests Its Involvement During Host Invasion.Frontiers in microbiology · 2018Article
- K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity.BMC bioinformatics · 2017Article
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1 author.
Funding
Abstract
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 important consideration. Here, I review the software available for analysis of RNA-Seq data for differential splicing and discuss intrinsic challenges for differential splicing analyses. Three approaches to differential splicing analysis are described, along with their associated software implementations, their strengths, limitations, and caveats. Suggestions for future work include more extensive experimental validation to assess accuracy of the software predictions and consensus formats for outputs that would facilitate visualizations, data exchange, and downstream analyses.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.