tappAS

tappAS: Your application to understand the functional implications of alternative splicing

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Features

Projects

tappAS is project based: You create a project, input your data, and then work with it

Data Analysis

Once you’ve created a project, tappAS provides a large selection of tools to help you analyse your data

Data Visualization

tappAS provides a comprehensive set of data visualization tools to help you recognize patterns and better understand the data

What is tappAS?

What is tappAS?

-tappAS is a Java GUI application for the analysis of RNA-Seq data down to the isoform level
-It provides a comprehensive set of data analysis, visualization, filtering, and hoc query tools
-It will run on most modern computers, provided they have enough computational resources and storage
-Best of all, tappAS is FREE for non-commercial use

Projects

-tappAS is project based: You create a project, input your data, and then work with it
-You need three files to create a project: an experimental design file, a transcript level expression, matrix and the corresponding annotation file
-tappAS provides annotation files for multiple species. You may use one of them or provide your own
-Data normalization and filtering options for expression levels and transcripts are provided

Projects
Data Analysis

Data Analysis

Once you’ve created a project, tappAS provides a large selection of tools to help you analyse your data:

-Differential Splicing Analysis (DSA)
-Annotation Features Differential Splicing Analysis (FDSA)
-Differential PolyadenylationSite (DPA)
-Annotation Features Diversity Analysis
-Differential Expression Analysis (DEA)
-Gene Set Enrichment Analysis (GSEA)
-Functional Enrichment Analysis (FEA) including Clustering Analysis.

Data analysis is provided for case-control and single or multiple time-course experiments. Alternative splicing information is important for understanding RNA-Seq data: in addition to gene level data analysis, tappAS tools provide data analysis at the isoform level.

Data Visualization

tappAS provides a comprehensive set of data visualization tools to help you recognize patters and better understand the data:

-Summary plots and charts.
-Distribution charts.
-Annotation features visualization for genes, transcripts, and proteins.
-Expression data density and PCA plots.
-Cluster network graph.
-GO terms directed acyclic graphs.
-Venn Diagrams.
-Miscellaneous data visualization.

Data Visualization
Other Features

Other Features

Using JavaFX as its platform, TAPPAS provides the rich set of features expected from a modern GUI application:

-Data tables with customizable columns, sorting, and filtering.
-Ability to export all application data and images to file.
-Resizable windows and zooming.
-Context-sensitive help and menus.
-Data drill downs.
-Display customization.
-Individual projects tabs.
-And lots of other features…

Requirements and Installation

What you need to have:
-A computer with up-to-date GUI version of Linux or Unix, Mac or Windows
-Minimum of 8GB of memory and 4 CPU cores
-Adequate amount 20GB or more, of unused disk space
-An up-to-date version of the Java Runtime Environment (JRE)
-An up-to-date version of R along with a few statistical packages
What you need to do:
-To install, just download the file and decompress it
-To run the application, double click the tappas.jar file

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Requirements and Installation