CCLE TreatmentResponse Snakemake

Authors: Jermiah Joseph

Contact: bhklab.jermiahjoseph@gmail.com

Description: Snakemake pipeline to curate and prepare the CCLE drug resonse data only.

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📦 Download

You can download the latest processed treatmentResponseExperiment here:

➡️ Download RDS File

[!NOTE] If the file does not exist yet, look through the releases to find a release that contains the file.

General Information

This work splits up the CCLE pipeline to focus only on the drug response data. The old pipeline can be found here BHKLAB-DataProcessing/CCLE-Pharmacoset_Snakemake

TODO

  • [ ] configure containers for the R packages

Set Up

Prerequisites

Pixi is required to run this project. If you haven't installed it yet, follow these instructions

Installation

  1. Clone this repository to your local machine
  2. Navigate to the project directory
  3. Set up the environment using Pixi:
pixi install

Documentation

Click here to view the full documentation