====== betAS ======

**intuitive analysis and visualisation of differential alternative splicing** \\
//by// Mariana Ascensão-Ferreira [[marianaascferreira@medicina.ulisboa.pt|marianaascferreira@medicina.ulisboa.pt]] \\ and Rita Martins-Silva [[rita.silva@medicina.ulisboa.pt|rita.silva@medicina.ulisboa.pt]]\\

betAS is a user-friendly Shiny-based **[[https://compbio.imm.medicina.ulisboa.pt/app/betAS|Web App]]** and **[[https://github.com/DiseaseTranscriptomicsLab/betAS/tree/dev|R package]]** that allows intuitive analysis and **visualisation of differential alternative splicing** (AS) based on beta distributions.

Beta distributions are suitable to quantify inclusion proportions of alternative sequences, using RNA sequencing reads supporting their inclusion and exclusion as surrogates for the two distribution shape parameters. Each beta distribution has the inclusion proportion as mean value and is narrower when the read coverage is higher, facilitating the interpretability of its precision when plotted. betAS uses beta distributions to accurately model PSI values and their precision, and to quantitatively and visually compare AS between groups of samples.

//betAS// allows the analysis of user-provided tables with AS quantifications, such as those obtained by **vast-tools**, **rMATS** or **Whippet**, ranking differentially spliced events by a significance metric that incorporates the compromise between the uncertainty in individual sample estimates and the variability among replicates.


**Tutorial:** 
  * [[https://www.youtube.com/watch?v=h6Xj1eIO5OU | betAS Web App tutorial]]
  * [[https://diseasetranscriptomicslab.github.io/betAS/inst/betAS_tutorial.html | betAS command-line interface (CLI) tutorial]]

**Mariana Ascensão-Ferreira**, **Rita Martins-Silva**, Nuno Saraiva-Agostinho and Nuno L. Barbosa-Morais (2024). "betAS: intuitive analysis and visualisation of differential alternative splicing using beta distributions". RNA 30:337–353
[[https://doi.org/10.1261/rna.079764.123 |DOI: 10.1261/rna.079764.123]].


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