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# tappAS: a user-friendly application to analyze the functional implications of alternative splicing. | ||
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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. | ||
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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. | ||
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[![DOI](https://zenodo.org/badge/255313071.svg)](https://zenodo.org/badge/latestdoi/255313071) | ||
This repository contains the source code of the tappAS application. | ||
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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. | ||
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[![DOI](https://zenodo.org/badge/255313071.svg)](https://zenodo.org/badge/latestdoi/255313071). | ||
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### 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. | ||
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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/). | ||
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**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. | ||
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### Documentation | ||
Documentation and videotutorials can be found at https://app.tappas.org/ (site under development). | ||
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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. | ||
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### 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. | ||
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If in need of further support, please contact: | ||
* **Pedro Salguero:** installation information, errors and software-related support: [email protected] | ||
* **Ángeles Arzalluz-Luque:** information related to analysis/results interpretation and questions on | ||
how to apply tappAS functionalities to your data: [email protected] | ||
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### License and copyright | ||
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