Cancer Omics and Drug Experiment Response Data (`coderdata`) Python Package

Usage

Datasets

Broad Sanger CPTAC HCMI BeatAML MPNST

Resources

GitHub FigShare PyPI Contribution Guide Deep Learning Tutorial Drug Response Tutorial Data Exploration Tutorial

Contribute

Introduction

CoderData is a cancer benchmark data package developed in Python and R. There are two aspects of this package, the backend build section and the user facing python package. The build section is a github workflow that generates four cancer datasets in a format that is easy for users and algorithms to ingest. The python package allows users to easily download the data, load it into python and reformat it as desired.

Installation and Usage

Bash / Command Line

To install coderdata, simply run the following command in your terminal:

pip install coderdata

Bash / Command line

To download datasets, simply run the following command in your terminal. Remove the prefix argument if you’d like to install all datasets.

coderdata download --prefix hcmi

Python

To download, load, and call datasets in python, simply run the following commands.

View our Usage page for full instructions.

Datasets

Data Overview