Merge branch 'dev' of https://github.com/DiseaseTranscriptomicsLab/betAS into dev

Author: ritamtbsilva

README.md

@@ -4,9 +4,33 @@
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-betAS is a user-friendly R package that allows intuitive analysis and
+**Please note that you are currently in the development branch.**
+**This README file is under active maintenance**
+
+
+
+> **Original article:** 
+>
+> Mariana Ascensão-Ferreira, Rita Martins-Silva, Nuno Saraiva-Agostinho and Nuno L. Barbosa-Morais (2023).
+> [betAS: intuitive analysis and visualisation of differential alternative splicing using beta distributions]([url](https://www.biorxiv.org/content/10.1101/2022.12.26.521935v2)). *bioRxiv*
+
+
+betAS is a user-friendly **R package** and **Shiny App** that allows intuitive analysis and
 visualisation of differential alternative splicing (AS) based on
-beta distributions. (This is the developing version/branch.)
+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.
+
+![Differential alternative splicing analysis in *betAS*](man/figures/betAS_screenshot.png)
 
 
 ## Tutorials
@@ -23,20 +47,13 @@ You can install the development version of betAS from [GitHub](https://github.co
 ``` r
 # install.packages("devtools")
 devtools::install_github("DiseaseTranscriptomicsLab/betAS@dev")
-```
-
-## Example
-
-This is a basic example which shows you how to solve a common problem:
-
-``` r
 library(betAS)
-## basic example code
 ```
 
+
 ## Feedback and support
 
-Please send any feedback and questions on betAS to:
+Please send any feedback and questions on *betAS* to:
 
 > Mariana Ascensão-Ferreira ([marianaascferreira@medicina.ulisboa.pt][email])
 >