Phenozip is a flexible tool for manipulating DEPI datasets.

See the quick-start guide below to get started using Phenozip.

Full javadocs can be found here.

CAAPP bitbucket account holders can access the latest Phenozip source code here

Installation

1. Install the latest version of Java.
2. Download Phenozip.jar
3. Double-click the jarfile you downloaded.

Combine and Anotate Results

Use the "Browse..." button at the top-right of the user interface to select any directory that contains DEPI experiment results.

Use the checkboxes as appropriate (typically check the top three boxes). As you make your selections, the "Info" and "Log" tabs will display the recognized result spreadsheets.

Click "Run Script". Combined and annotated results will be saved directly in the directory you selected. Any warnings or errors will appear in the "Log" tab.

Package Results

Check "Zip combined results" to also create a zip archive containing relevent spreadsheets after combining.

Check "Insert results to a new SQLite DB" to create an SQLite Database file that can be shared and accessed in a variety of ways.

Create and Run a Custom Script

As you pick settings using the user interface, the "Script" tab is automatically updated.

Here, scripts can be manually modified, copied-and-pasted, combined, etc.

Use the "File" menu under the "Scripts" tab to save and load scripts.

You can run a script headlessly from the command line (e.g. as a part of an automated pipeline).

java -jar Phenozip.jar scriptFile.txt