ArticleBioinformatics (Oxford, England)2018
MAJIQ-SPEL: web-tool to interrogate classical and complex splicing variations from RNA-Seq data.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- EPBAM: annotation-robust detection of alternative splicing events and a systematic benchmarking of current tools.Briefings in bioinformatics · 2026Article
- Myocardial Recovery With Mechanical Circulatory Support Is Linked to Alternative Splicing and Subcellular Localization of CAMK2D.Circulation · 2026Article
- Optimizing 2D in vitro differentiation conditions for C2C12 murine myoblasts on gelatin hydrogel.Journal of muscle research and cell motility · 2025Article
- Cytoplasmic CaMKIIδ-B prevents myocardial recovery in heart failure.bioRxiv : the preprint server for biology · 2025Article
- iPSC motor neurons, but not other derived cell types, capture gene expression changes in postmortem sporadic ALS motor neurons.Cell reports · 2023Article
- RNA splicing analysis using heterogeneous and large RNA-seq datasets.Nature communications · 2023Article
- RNA-seq data science: From raw data to effective interpretation.Frontiers in genetics · 2023Review
- Modulation of pre-mRNA structure by hnRNP proteins regulates alternative splicing ofScience advances · 2022Article
- Cell environment shapes TDP-43 function with implications in neuronal and muscle disease.Communications biology · 2022Article
- Computational cancer neoantigen prediction: current status and recent advances.Immuno-oncology technology · 2021Review
- IRFinder-S: a comprehensive suite to discover and explore intron retention.Genome biology · 2021Article
- Implications of Antigen Selection on T Cell-Based Immunotherapy.Pharmaceuticals (Basel, Switzerland) · 2021Review
- Article
- Strategies to Uplift Novel Mendelian Gene Discovery for Improved Clinical Outcomes.Frontiers in genetics · 2021Review
- Alternative Splicing During theG3 (Bethesda, Md.) · 2020Article
- The how and why of lncRNA function: An innate immune perspective.Biochimica et biophysica acta. Gene regulatory mechanisms · 2020Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
summaryAnalysis 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 events are complex, resulting in numerous possible isoforms that quickly become difficult to visualize, interpret and experimentally validate. To address these challenges we developed MAJIQ-SPEL, a web-tool that takes as input local splicing variations (LSVs) quantified from RNA-Seq data and provides users with visualization and quantification of gene isoforms associated with those. Importantly, MAJIQ-SPEL is able to handle both classical (binary) and complex, non-binary, splicing variations. Using a matching primer design algorithm it also suggests to users possible primers for experimental validation by RT-PCR and displays those, along with the matching protein domains affected by the LSV, on UCSC Genome Browser for further downstream analysis. AVAILABILITY AND IMPLEMENTATION: Program and code will be available at http://majiq.biociphers.org/majiq-spel. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.