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The following video explains GeMSE's mission, and more videos explaining how to use it, are at this playlist.

Documentation

1. Interface
2. Load data
3. Transitions
4. Dendrogram Panel
5. Pattern Exploration
6. Connect to R

Requirements

The GeMSE application is packed with all its dependencies. However, you need to do the following setups:

• make sure Java Runtime Environment (version 8 or newer) is installed. You can download it from here.
• [Optional] configure R.

Quick start

1. Download the three dummy files from this page.
2. Download the latest version of GeMSE, and run it by double clicking on the file.
3. Goto File > Load, and in the opened window, browse to the folder in which the files of step #1 are downloaded.
4. Make sure the file type is set to Browser Extensible Data (BED).
5. Select the three files, and click Open.
6. Uncheck the Value is numeric, and read the column check box.
7. Click Next Column.
8. Check the Value is numeric, and read the column check box.
9. Click OK.
10. Click YES.
11. Click Create Genometric Space button.

See this video on how to load the files.

Download Sample Data

(See this page on how to load files)

• Download three dummy homogeneous files from here, and three dummy heterogeneous files and a reference sample from here (what are homogeneous/heterogeneous files?). See this video on how to load these files.

• Download real data and metadata from this page. These files were originally downloaded from ENCODE (links to the source files), then are processed using MuSERA (using this at-Job file). See [this video] for how GeMSE facilitates exploring these files.

Use-case with Real Data

This video explains GeMSE functionalities using real data. The data used in this video are available from this page.