Hartwig Biomarkers

Goal of Repository

Clean and organize the Hartwig Medical Foundation data request files into a single dataframe.
See Hartwig Medical Foundation: https://www.hartwigmedicalfoundation.nl/en/

Organization

For each file type, a pipeline computes and organizes features across all samples.
Output from each pipeline are then joined by their sample ids.

Prerequisites to Run

Hartwig Data Request Approval

Data request: https://www.hartwigmedicalfoundation.nl/en/data/data-access-request/
PURPLE, ISOFOX, and clinical data output.

Source and reference data

Run and tested on Hartwig data request files shared on August 9, 2022.
Source directory locations need to be specified in mission_control/treasure_map.*.

QMap and conda environments

Jobs are submitted with the QMap tool from the bbglab: https://github.com/bbglab/qmap
QMap tool calls two conda environments, stored in conda_env folder.

Run the pipeline

From the root directory:

$ python run.py