immunoscore_results_aggregator

• Extracts and aggregates results from the definiens immunoscore plugin to enable validation of region of interest selection and of hotspots
• Uploads results to a nosql database (mongodb)

Enables exporting of results as:

• Properly structured data directory containing essential files for review
• As a CSV statistics summary file containing datasets for further analysis (e.g. R)

Mongodb datastructure

Example of immunoscore qa/qc entries:

Example of data structure of each entry:

Each entry contains file paths, a binary blob of the relevant snapshot, case number and relevant annotation.

Requirements

 *nix
 ruby >= 1.9.3
 mongodb

Installation

gem install immunoscore_results_aggregator

Setup

Edit config.rb to setup the root of the immunoscore directory tree, choose a mongodb name, and a name for the results export directory

immunoscore_cli.rb show_config
immunoscore_cli.rb edit_config

Run

immunoscore_cli.rb
Follow help intructions