oncoEnrichR use cases

Published June 17, 2023 | Version v1.7

Dataset Open

1. Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Norway
2. ELIXIR Norway, Department of Informatics, University of Oslo, Norway
3. Early Computational Oncology, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
4. Centre for Bioinformatics, Department of Informatics, University of Oslo, Norway

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 <LOCAL_DIRECTORY>/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

Files

Name	Size	Download all
oncoenrichr_use_cases.zip md5:13f0747fdce81a6da273bc572ca2767a	25.9 MB	Preview Download