ReviewNature protocols2024
rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data.
Review in Nature protocols, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 186 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
186 citing papers in PubMed, 209 citations in OpenAlex.
- Clinical response to azacitidine in MDS is associated with distinct DNA methylation changes in HSPCs.Nature communications · 2025Trial
- RBMS1 Contributes to Early Arteriovenous Fistula Neointimal Remodeling Through Modulation of VSMC Phenotypic Responses.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- TCASIA: an integrative atlas linking alternative splicing landscapes for cancer immunotherapy.Journal for immunotherapy of cancer · 2026Article
- Splicing genes as main targets of differential splicing.G3 (Bethesda, Md.) · 2026Article
- Review
- Lateralized Gene Splicing in the Brain is Associated With Lateralized Feeding Behavior in an Asymmetrical Scale-eating Cichlid Fish.Genome biology and evolution · 2026Article
- HnRNPK restrains memory precursor and plasma cell differentiation to control germinal center B-cell output.Cellular & molecular immunology · 2026Article
- Transcriptome sequencing of Bacillus sp. HMM and effect of GH gene overexpression on cellulase activities.Biotechnology letters · 2026Article
- PRMT1-SFPQ regulates intron retention to control matrix gene expression during craniofacial development.eLife · 2026Article
- De novo variants in the poly(rC)-binding protein gene PCBP1 cause a neurodevelopmental disorder.Molecular psychiatry · 2026Article
- Systems genetics approaches model the heritable architecture of polyendocrine metabolic ovarian syndrome.The Journal of clinical investigation · 2026Article
- RAISE quantifies RNA binding protein activity via transcriptomic profiling.Nature communications · 2026Article
- Cardiac fibroblast deletion of PTBP1 modulates the profibrotic response by alternative splicing.Nature communications · 2026Article
- CDK12/13 inhibition overcomes platinum resistance by impairing RNA metabolism.Signal transduction and targeted therapy · 2026Article
- DRIVE: a comprehensive resource deciphering drug-induced transcriptomic and splicing response in cancer cell.Neoplasia (New York, N.Y.) · 2026Article
- CPEB1 orchestrates cell cycle-dependent translation of maternal factors to coordinate nuclear-cytoplasmic maturation in porcine oocytes.Science China. Life sciences · 2026Article
- EPBAM: annotation-robust detection of alternative splicing events and a systematic benchmarking of current tools.Briefings in bioinformatics · 2026Article
- Human TDP-43 expression worsens FTD-related phenotypes in progranulin-insufficient mice.Neurobiology of disease · 2026Article
- Targeting PRMT5 Inhibitor-Induced Adaptation in Pancreatic Cancer with the RBM39 Degrader Indisulam.Cancer research communications · 2026Article
- Spatial Total RNA Sequencing of Formalin-Fixed Paraffin-Embedded Tissue by spRandom-seq.Small (Weinheim an der Bergstrasse, Germany) · 2026Article
126 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Pre-mRNA alternative splicing is a prevalent mechanism for diversifying eukaryotic transcriptomes and proteomes. Regulated alternative splicing plays a role in many biological processes, and dysregulated alternative splicing is a feature of many human diseases. Short-read RNA sequencing (RNA-seq) is now the standard approach for transcriptome-wide analysis of alternative splicing. Since 2011, our laboratory has developed and maintained Replicate Multivariate Analysis of Transcript Splicing (rMATS), a computational tool for discovering and quantifying alternative splicing events from RNA-seq data. Here we provide a protocol for the contemporary version of rMATS, rMATS-turbo, a fast and scalable re-implementation that maintains the statistical framework and user interface of the original rMATS software, while incorporating a revamped computational workflow with a substantial improvement in speed and data storage efficiency. The rMATS-turbo software scales up to massive RNA-seq datasets with tens of thousands of samples. To illustrate the utility of rMATS-turbo, we describe two representative application scenarios. First, we describe a broadly applicable two-group comparison to identify differential alternative splicing events between two sample groups, including both annotated and novel alternative splicing events. Second, we describe a quantitative analysis of alternative splicing in a large-scale RNA-seq dataset (~1,000 samples), including the discovery of alternative splicing events associated with distinct cell states. We detail the workflow and features of rMATS-turbo that enable efficient parallel processing and analysis of large-scale RNA-seq datasets on a compute cluster. We anticipate that this protocol will help the broad user base of rMATS-turbo make the best use of this software for studying alternative splicing in diverse biological systems.
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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.