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.
This source code is available as a compiled, user-ready application. To obtain the latest version of the tappAS, please acess the Releases section and download the tappAS.jar file.
For further installation instructions and information on compatibility and dependencies, see the Install file or visit the tappAS website.
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 and videotutorials can be found at https://app.tappas.org/ (site under development).
Users are welcome to follow our recorded ISMB2020 tutorial, in which we describe the tappAS application in detail, and demonstrate how to run and interpret some of the analysis. Necessary data and slides can be downloaded here.
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.
If you have questions about how to best use tappAS with your data, please check our Frequently Asked Questions section for common use cases (most of the questions we routinely receive from users have been answered in FAQs).
If you encounter a bug or error using or installing tappAS, please open an Issue to report it.
If in need of further support, please contact:
- Alessandra Martínez: alessandra.martinez.m [at] gmail.com
tappAS is published and fully demonstrated in our Genome Biology manuscript. If you use tappAS for your study, please cite:
- de la Fuente, L., Arzalluz-Luque, Á., Tardáguila, M. et al. tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing. Genome Biol 21, 119 (2020). https://doi.org/10.1186/s13059-020-02028-w
Copyright (C) 2020, de la Fuente et al.
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
A copy of the GNU General Public License is provided along with this program (see LICENSE file).
