rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data
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Summary
A new statistical model and computer program, replicate MATS (rMATS), designed for detection of differential alternative splicing from replicate RNA-Seq data, which uses a hierarchical model to simultaneously account for sampling uncertainty in individual replicates and variability among replicates.
- Type
- article
- Published
- 2014-12-05
- Cited by
- 2,382
- References
- 37
- Access
- Open access
- OpenAlex
- https://openalex.org/W2066231767
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:11338913
Keywords
Replicate, RNA-Seq, Computational biology, RNA, Alternative splicing
References
- Analysis and design of RNA sequencing experiments for identifying isoform regulation
- Methods to study splicing from high-throughput RNA sequencing data.
- Sequencing technology does not eliminate biological variability
- RNA-Seq: a revolutionary tool for transcriptomics
- Alternative splicing and evolution: diversification, exon definition and function
- Statistical Design and Analysis of RNA Sequencing Data
- Detection and Removal of Biases in the Analysis of Next-Generation Sequencing Reads
- Transcriptome-wide Landscape of Pre-mRNA Alternative Splicing Associated with Metastatic Colonization
- Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
- Modeling non-uniformity in short-read rates in RNA-Seq data
- Functional consequences of developmentally regulated alternative splicing
- rSeqDiff: Detecting Differential Isoform Expression from RNA-Seq Data Using Hierarchical Likelihood Ratio Test
- DiffSplice: the genome-wide detection of differential splicing events with RNA-seq
- Expansion of the eukaryotic proteome by alternative splicing
- Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
- Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues
- Splicing in disease: disruption of the splicing code and the decoding machinery
- MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data
- Tumor-specific isoform switch of the fibroblast growth factor receptor 2 underlies the mesenchymal and malignant phenotypes of clear cell renal cell carcinomas
- GLiMMPS: robust statistical model for regulatory variation of alternative splicing using RNA-seq data
Cited by
- A brief review of single-cell transcriptomic technologies.
- Genome-scale analysis identifies paralog lethality as a vulnerability of chromosome 1p loss in cancer
- Splicing modulation as novel therapeutic strategy against diffuse malignant peritoneal mesothelioma
- iREAD: a tool for intron retention detection from RNA-seq data
- nagnag: Identification and quantification of NAGNAG alternative splicing using RNA‐Seq data
- Novel splice isoforms of dairy goat DBC1 and their diverse mRNA expression profiles
- Leveraging transcript quantification for fast computation of alternative splicing profiles
- Disease-associated mutation in SRSF2 misregulates splicing by altering RNA-binding affinities
- Strand specific RNA-seq data for higher specificity
- Vision from next generation sequencing: Multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease
- How are Bayesian and Non-Parametric Methods Doing a Great Job in RNA-Seq Differential Expression Analysis? : A Review
- Discover hidden splicing variations by mapping personal transcriptomes to personal genomes
- The splicing regulators Esrp1 and Esrp2 direct an epithelial splicing program essential for mammalian development
- Advanced Applications of RNA Sequencing and Challenges
- Detection and Visualization of Differential Exon and Splice Junction Usage in RNA-Seq Data with JunctionSeq
- A survey of best practices for RNA-seq data analysis
- Differential transcript usage from RNA-seq data: isoform pre-filtering improves performance of count-based methods
- A new view of transcriptome complexity and regulation through the lens of local splicing variations
- SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data
- Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage
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