ArticleBriefings in bioinformatics2020
Systematic evaluation of differential splicing tools for RNA-seq studies.
Article in Briefings in bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 107 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.
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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
107 citing papers in PubMed.
- Splicing genes as main targets of differential splicing.G3 (Bethesda, Md.) · 2026Article
- Review
- RNA splicing and cardiovascular disease: a guide for cardiologists.European heart journal · 2026Review
- Benchmarking RNA-seq with the Quartet and MAQC reference materials to establish best practices for accurate alternative splicing analysis.Nature communications · 2026Article
- Tools and tactics for studying alternative splicing.Nature reviews. Genetics · 2026Review
- The impact of read depth and read length on RNA-seq splicing analysis.RNA (New York, N.Y.) · 2026Article
- Investigating Alzheimer's Disease-Associated Genes Using Differential Splicing Frequency Analysis.Cells · 2026Article
- Role of alternative splicing in cancer progression.Irish journal of medical science · 2026Review
- Shared splicing dysregulation in heart failure associated with dilated and ischaemic cardiomyopathy and spatial specificity across cardiac regions.Cardiovascular research · 2026Article
- Alternatively spliced STIM2.3 is an evolutionarily late store-operated Ca2+ entry regulator expressed in brain.Journal of cell science · 2026Article
- The IR-Homeostat Hypothesis: Intron Retention as an Evolutionarily Conserved Fine-Tuning Layer and a Reversible Blood Biomarker of Homeostatic Dysregulation in Mood Disorders.International journal of molecular sciences · 2026Review
- Exercise modulation of the alternative splicing landscape in human tissues.bioRxiv : the preprint server for biology · 2026Article
- Designing RNA sequencing experiments: A practical guide to reproducible gene expression analysis.Computational and structural biotechnology journal · 2026Review
- Splicing across adipocyte differentiation is highly dynamic and impacted by the metabolic phenotype.iScience · 2025Article
- Determining off-target effects of splice-switching antisense oligonucleotides using short read RNAseq in neuronally differentiated human induced pluripotent stem cells.Human molecular genetics · 2025Article
- RPS24 microexon isoform as a novel biomarker for estrogen receptor-positive breast cancer progression and therapeutic resistance.Experimental & molecular medicine · 2025Article
- SpliceDecoder: A High-Throughput Tool for Guiding the Functional Interpretation of Differential Splicing Events.bioRxiv : the preprint server for biology · 2025Article
- Characterization of aberrant splicing in pediatric central nervous system tumors revealsbioRxiv : the preprint server for biology · 2025Article
- Article
- Hybridization and gene expression: Beyond differentially expressed genes.Molecular ecology · 2025Review
47 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.
Funding
Abstract
Differential splicing (DS) is a post-transcriptional biological process with critical, wide-ranging effects on a plethora of cellular activities and disease processes. To date, a number of computational approaches have been developed to identify and quantify differentially spliced genes from RNA-seq data, but a comprehensive intercomparison and appraisal of these approaches is currently lacking. In this study, we systematically evaluated 10 DS analysis tools for consistency and reproducibility, precision, recall and false discovery rate, agreement upon reported differentially spliced genes and functional enrichment. The tools were selected to represent the three different methodological categories: exon-based (DEXSeq, edgeR, JunctionSeq, limma), isoform-based (cuffdiff2, DiffSplice) and event-based methods (dSpliceType, MAJIQ, rMATS, SUPPA). Overall, all the exon-based methods and two event-based methods (MAJIQ and rMATS) scored well on the selected measures. Of the 10 tools tested, the exon-based methods performed generally better than the isoform-based and event-based methods. However, overall, the different data analysis tools performed strikingly differently across different data sets or numbers of samples.
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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.