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Comprehensive and scalable quantification of splicing differences with MntJULiP

Guangyu Yang, Sarven Sabunciyan, Liliana Florea
doi: https://doi.org/10.1101/2020.10.26.355941
Guangyu Yang
1Department of Computer Science, Johns Hopkins University, Baltimore MD
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Sarven Sabunciyan
2Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore MD
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Liliana Florea
1Department of Computer Science, Johns Hopkins University, Baltimore MD
3McKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore MD
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  • For correspondence: florea@jhu.edu
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Abstract

Alternative splicing of mRNA is an essential gene regulatory mechanism with important roles in development and disease. We present MntJULiP, a method for comprehensive and accurate quantification of splicing differences between two or more conditions. MntJULiP implements novel Dirichlet-multinomial and zero-inflated negative binomial models within a Bayesian framework to detect both changes in splicing ratios and in absolute splicing levels of introns with high accuracy, and can find classes of variation overlooked by reference tools. Additionally, a mixture model allows multiple conditions to be compared simultaneously. Highly scalable, it processed hundreds of GTEx samples in <1 hour to reveal splicing constituents of tissue differentiation.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/Splicebox/MntJULiP

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 27, 2020.
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Comprehensive and scalable quantification of splicing differences with MntJULiP
Guangyu Yang, Sarven Sabunciyan, Liliana Florea
bioRxiv 2020.10.26.355941; doi: https://doi.org/10.1101/2020.10.26.355941
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Comprehensive and scalable quantification of splicing differences with MntJULiP
Guangyu Yang, Sarven Sabunciyan, Liliana Florea
bioRxiv 2020.10.26.355941; doi: https://doi.org/10.1101/2020.10.26.355941

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