eXamine

This stand-alone version of eXamine derives from the Cytoscape app eXamine. It supports a set-oriented visual analysis approach for annotated network modules. These network modules are displayed as node-link diagrams with colored contours on top to depict sets of nodes that share an annotation.

Screenshot

Install

You can:

Download a binary release directly.
Compile eXamine yourself, as described below.

Run

Run eXamine as follows, where your current working directory has to contain a folder data-sets with your data:

java -jar eXamine.jar

Datasets

Datasets are placed in a folder data-sets, in the current working directory, and show up as tabs on the left side in eXamine. Each data set has a folder that contains three types of files in tab-separated format:

*.nodes lists the nodes of the network, with a unique Identifier, a Symbol that is displayed on the node, one or multiple scores that are visualized as the node’s contour with a divergent colormap, and a URL that links to more information when the node is clicked. See Exemplar-1/proteins.nodes for an example.
*.links lists the undirected node-to-node links, as pairs of node identifiers, that form the network. See Exemplar-1/interactions.links for an example.
*.annotations lists the annotations, or sets of nodes, that cover parts of this network. Each annotation has a unique Identifier, a Symbol that is displayed in the annotation lists on the right side in eXamine, a Category that organizes the annotations into tabs on the right side in eXamine, a single Score that is displayed alongside the annotation, and a URL that links to more information if available. See Exemplar-1/go_and_kegg.annotations for an example.
*.memberships lists which nodes are covered by which annotations, as module-to-node pairs of identifiers. See Exemplar-1/go_and_kegg.memberships for an example.

The Module Category of annotations should always be present, as you can see in Exemplar-1/modules.annotations. Any node displayed by eXamine is present in at least one of these modules. eXamine will not show any node if there are no Module annotations.

You can partition the files of a dataset. For example, the links of your network can be split across multiple *.link files. However, the identifiers of nodes and annotations have to be unique within the entire dataset, these are not scoped by file.

Compile

Requires (Open) JDK 1.7 or higher: https://openjdk.java.net/install

Linux:
```
sudo apt-get install default-jdk
```
Mac:
```
brew install openjdk
```
Requires Apache Maven 3.8 or higher: https://maven.apache.org/download.cgi

Linux:
```
sudo apt-get install maven
```
Mac:
```
brew install maven
```

Get eXamine from GitHub:

git clone <HTTPS clone URL (see on the right side of this page)>

Compile eXamine:
```
cd eXamine-stand-alone
mvn install
```
This results in eXamine.jar in the eXamine-stand-alone folder.