ArticleNAR genomics and bioinformatics2023
Alternative splicing analysis benchmark with DICAST.
Article in NAR genomics and bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
11 citing papers in PubMed.
- TCASIA: an integrative atlas linking alternative splicing landscapes for cancer immunotherapy.Journal for immunotherapy of cancer · 2026Article
- 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
- Shared splicing dysregulation in heart failure associated with dilated and ischaemic cardiomyopathy and spatial specificity across cardiac regions.Cardiovascular research · 2026Article
- Neurofibromin 1 (International journal of molecular sciences · 2026Article
- RNA-based diagnostic studies in genetics: Review and guidance from a multidisciplinary French network.European journal of human genetics : EJHG · 2025Review
- KDASDB: A comprehensive and user-friendly database of alternative splicing dedicated to kidney diseases.Computational and structural biotechnology journal · 2025Article
- Differential quantification of alternative splicing events on spliced pangenome graphs.PLoS computational biology · 2024Article
- Mining alternative splicing patterns in scRNA-seq data using scASfind.Genome biology · 2024Article
- Prediction of tumor-specific splicing from somatic mutations as a source of neoantigen candidates.Bioinformatics advances · 2024Article
- Alternative Transcripts Diversify Genome Function for Phenome Relevance to Health and Diseases.Genes · 2023Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alternative splicing is a major contributor to transcriptome and proteome diversity in health and disease. A plethora of tools have been developed for studying alternative splicing in RNA-seq data. Previous benchmarks focused on isoform quantification and mapping. They neglected event detection tools, which arguably provide the most detailed insights into the alternative splicing process. DICAST offers a modular and extensible framework for analysing alternative splicing integrating eleven splice-aware mapping and eight event detection tools. We benchmark all tools extensively on simulated as well as whole blood RNA-seq data. STAR and HISAT2 demonstrated the best balance between performance and run time. The performance of event detection tools varies widely with no tool outperforming all others. DICAST allows researchers to employ a consensus approach to consider the most successful tools jointly for robust event detection. Furthermore, we propose the first reporting standard to unify existing formats and to guide future tool development.
Identifiers
What OpenQuestion holds
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.