oncoEnrichR use cases

Use case analyses - oncoEnrichR

This Zenodo repository hosts two use case output reports from oncoEnrichR, a dedicated tool for geneset interpretation in cancer.

Directory structure:

reports - holds pre-computed HTML reports and Excel woorkbooks for two use cases

FGFR1 network (protein proximity screen)

fgfr1_network_oncoEnrichR.v1.4.1.html

fgfr1_network_oncoEnrichR.v1.4.1.xlsx

EGFRi drug resistance drivers (CRISPR screen)

egfr_drug_resistance_oncoEnrichR.v1.4.1.html

egfr_drug_resistance_oncoEnrichR.v1.4.1.xlsx

input - holds input data for the two use cases
  1. fgfr1_network_input.tsv
  2. egfr_drug_resistance_input.tsv

docker - holds input and code for re-running use case analyses through
  a Docker container

Instructions

Install Docker on your local computer/client (OS X/Linux)

Download the input and output directory of the docker directory to your local computer/client

Pull the Docker image with the following Docker command on the command-line:

docker pull sigven/oeusecase:latest

Run the use case analyses with the following Docker command:

docker run --rm -ti -v /input:/input -v /LOCAL_DIRECTORY/output:/output sigven/oeusecase:latest

NOTE: replace LOCAL_DIRECTORY with the full path on your local computer where you have downloaded the input and output folders

The above command will generate HTML reports and Excel workbooks for the two use cases in the output directory