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 # tappAS: a user-friendly application to analyze the functional implications of alternative splicing.
 
-This repository contains the source code of the tappAS application, version 1.0.0. TappAS is a bioinformatics application
-featuring a Graphical User Interface, developed in Java and R. 
-
-To obtain the compiled, user-ready version of the application and consult related documentation, 
-visit  https://app.tappas.org/, or go to the Release section to download the tappAS.jar file.
-
-[![DOI](https://zenodo.org/badge/255313071.svg)](https://zenodo.org/badge/latestdoi/255313071)
+This repository contains the source code of the tappAS application. 
+
+TappAS is a bioinformatics application containing a wide range of analyses to evaluate the functional
+impact of Alternative Transcript Expression Mechanisms (AltTEM), in the form of a GUI application 
+developed in Java and R. To do this, tappAS relies on A) a series of statistical methods to evaluate different aspects
+of post-transcriptional processing and B) a functional annotation file containing positional information for functional
+motifs and domains at the transcript and CDS levels.
+
+[![DOI](https://zenodo.org/badge/255313071.svg)](https://zenodo.org/badge/latestdoi/255313071).
+
+### Installation
+This source code is available as a compiled, user-ready application.
+To obtain the latest version of the tappAS, please acess the [Releases section](https://github.com/ConesaLab/tappAS/releases) 
+and download the *tappAS.jar* file.
+
+For further installation instructions and information on compatibility 
+and dependencies, see [the Install file](https://app.tappas.org/resources/downloads/install.pdf) or visit the 
+[tappAS website](https://app.tappas.org/).
+
+**WARNING: any release of tappAS < 1.0.0 constitutes a beta version. Use at your own risk.** 
+If you were using version 0.99.15 or below, we recommend replacing it with tappAS 1.0.0 or above. 
+In this case, due to major changes in the application functioning, you'll need to delete the 
+*tappasWorkspace* folder and create all projects again. We apologize for any inconveniences.
+
+### Documentation
+Documentation and videotutorials can be found at https://app.tappas.org/ (site under development).
+
+Comprehensive information about the methods and graphics implemented in tappAS,
+their interpretation and how to run them can be found within the application. Each window and panel
+contains a **Help Menu** as a source of built-in documentation. To access it, 
+click the [**?**] icon available in the different windows and panels.
+
+### Contact
+If you encounter a bug or error using or installing tappAS, 
+please [open an Issue](https://github.com/ConesaLab/tappAS/issues) to report it.
+
+If in need of further support, please contact:
+* **Pedro Salguero:** installation information, errors and software-related support: pedsalga@upv.edu.es
+* **Ángeles Arzalluz-Luque:** information related to analysis/results interpretation and questions on 
+how to apply tappAS functionalities to your data: angeles.arzalluz@gmail.com
 
 
 ### License and copyright