ArticleGenome biology2020
BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 30 citations in OpenAlex.
- IsoformSwitchAnalyzeR v2: analysis of functional isoform changes in long-read and single-cell sequencing data.NAR genomics and bioinformatics · 2026Article
- Dysregulation of alternative splicing patterns in the ovaries of reproductively aged mice.Reproduction (Cambridge, England) · 2026Article
- Dividing out quantification uncertainty enables assessment of differential transcript usage with limma and edgeR.Nucleic acids research · 2025Article
- Computational methods for alternative polyadenylation and splicing in post-transcriptional gene regulation.Experimental & molecular medicine · 2025Review
- DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes.Biostatistics (Oxford, England) · 2024Article
- DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes.bioRxiv : the preprint server for biology · 2024Article
- Differential transcript usage analysis incorporating quantification uncertainty via compositional measurement error regression modeling.Biostatistics (Oxford, England) · 2024Article
- Quantifying transcriptome diversity: a review.Briefings in functional genomics · 2024Review
- Unveiling the Role of Dynamic Alternative Splicing Modulation After Infestation with Sea Lice (Caligus rogercresseyi) in Atlantic Salmon.Marine biotechnology (New York, N.Y.) · 2023Article
- A Bayesian model for unsupervised detection of RNA splicing based subtypes in cancers.Nature communications · 2023Article
- Compression of quantification uncertainty for scRNA-seq counts.Bioinformatics (Oxford, England) · 2021Article
- MOCCASIN: a method for correcting for known and unknown confounders in RNA splicing analysis.Nature communications · 2021Article
- Polee: RNA-Seq analysis using approximate likelihood.NAR genomics and bioinformatics · 2021Article
- Proteogenomic Workflow Reveals Molecular Phenotypes Related to Breast Cancer Mammographic Appearance.Journal of proteome research · 2021Article
- Streamlining differential exon and 3' UTR usage with diffUTR.BMC bioinformatics · 2021Article
- Article
- Probing Isoform Switching Events in Various Cancer Types: Lessons From Pan-Cancer Studies.Frontiers in molecular biosciences · 2021Review
- BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty.Genome biology · 2020Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alternative splicing is a biological process during gene expression that allows a single gene to code for multiple proteins. However, splicing patterns can be altered in some conditions or diseases. Here, we present BANDITS, a R/Bioconductor package to perform differential splicing, at both gene and transcript level, based on RNA-seq data. BANDITS uses a Bayesian hierarchical structure to explicitly model the variability between samples and treats the transcript allocation of reads as latent variables. We perform an extensive benchmark across both simulated and experimental RNA-seq datasets, where BANDITS has extremely favourable performance with respect to the competitors considered.
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