rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

By Shihao Shen, J. Park, Zhi-xiang Lu, Lan Lin, M. Henry, Ying Nian Wu, Qing Zhou, Yi Xing. Proceedings of the National Academy of Sciences of the United States of America, 2014

2,337 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f34897c8d816d11a98a7f2f8408d322021043234

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Citations in the corpus

A survey of best practices for RNA-seq data analysis (2016, background): “…on exons (and junctions) of the genes. rMATS detects differential usage of exons by comparing exon-inclusion levels defined with junction reads [71]. rDiff detects differential isoform expression by comparing read counts on alternative regions of the gene, either with or without annotated…”
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie, and Ballgown (2016, background): “We also note that although the protocol presented here detects differentially expressed transcripts and genes, it is not designed to detect differential exon usage alone, a task that several other programs (DEXseq 23 , rMATS 24 and MISO 25 ) have been developed specifically to address.”
CSCD: a database for cancer-specific circular RNAs (2017, methodology): “Potential alternative splicing events of a linear gene, including skipped exons, alternative 5’ splice site, alternative 3’ splice site, mutually exclusive exons and retained introns, were detected by rMATS (44) with default parameters.”
Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice (2019, background): “2.5) (Shen et al., 2014).”
SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions (2018, neutral): “These methods generally involve the analysis of either transcript isoforms [4–7], clusters of splice junctions [8, 9], alternative splicing events [10, 11], or exonic regions [12].”
Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma. (2018, neutral): “…Torres-Garcia et al., 2014 https://sourceforge.net/projects/prada/ pheatmap NA https://cran.r-project.org/web/packages/pheatmap/ rMATS Shen et al., 2014 http://rnaseq-mats.sourceforge.net/ RSEM Li and Dewey, 2011 https://deweylab.github.io/RSEM/ Samr Li and Tibshirani, 2013…”
Annotation-free quantification of RNA splicing using LeafCutter (2017, neutral): “We compared LeafCutter against other methods for differential splicing detection including Cufflinks2 5 , MAJIQ 12 , and rMATS 26 .”
RNA Sequencing Data: Hitchhiker's Guide to Expression Analysis (2018, methodology): “Some of the main DS tools based on PSIs include: rMATS [176] , which uses a LRT, and SUPPA2 [177] , whose test is based on comparing the observed difference in PSIs across conditions to the empirical cumulative density function of the withinreplicates differences of PSIs of splice junctions fro”